Ultima develop code merge

src/main/java/org/broad/igv/prefs/Constants.java

@@ -113,6 +113,7 @@ private Constants() {
     public static final String SAM_ALIGNMENT_SCORE_THRESHOLD = "SAM.ALIGNMENT_SCORE_THRESHOLD";
     public static final String SAM_COMPUTE_ISIZES = "SAM.COMPUTE_ISIZES";
     public static final String SAM_MAX_INSERT_SIZE_THRESHOLD = "SAM.INSERT_SIZE_THRESHOLD";
+    public static final String SAM_INSERT_QUAL_COLORING = "SAM.INSERT_QUAL_COLORING";
     public static final String SAM_MIN_INSERT_SIZE_THRESHOLD = "SAM.MIN_INSERT_SIZE_THRESHOLD";
     public static final String SAM_MAX_INSERT_SIZE_PERCENTILE = "SAM.ISIZE_MAX_PERCENTILE";
     public static final String SAM_MIN_INSERT_SIZE_PERCENTILE = "SAM.MIN_ISIZE_MIN_PERCENTILE";

src/main/java/org/broad/igv/sam/AlignmentBlock.java

@@ -69,4 +69,5 @@ default int getPadding() {
 
     char getCigarOperator();
 
+    default int getIndexOnRead() { return 0; }
 }

src/main/java/org/broad/igv/sam/AlignmentBlockImpl.java

@@ -42,6 +42,7 @@ public class AlignmentBlockImpl implements AlignmentBlock {
     private int pixelEnd;
     private int padding = 0;
     private char cigarOperator;
+    private int indexOnRead;
 
     public AlignmentBlockImpl(int start, byte[] bases, byte[] qualities) {
         this(start, bases, qualities, 0, bases.length, (char) 0);
@@ -57,6 +58,8 @@ public AlignmentBlockImpl(int start, byte[] bases, byte[] qualities, int offset,
         // qualities are optional in a SAMRecord, we might get null or an array of zero
         this.qualities = qualities == null || qualities.length == 0 ? EMPTY_ARRAY :  new ByteSubarray(qualities, offset, nBases, (byte) 126);
         this.cigarOperator = cigarOperator;
+
+        this.indexOnRead = offset;
     }
 
     @Override
@@ -177,4 +180,8 @@ public boolean hasBases() {
     public void setPadding(int padding) {
         this.padding = padding;
     }
+
+    public int getIndexOnRead() {
+        return this.indexOnRead;
+    }
 }

src/main/java/org/broad/igv/sam/AlignmentRenderer.java

@@ -35,6 +35,7 @@
 import org.broad.igv.prefs.IGVPreferences;
 import org.broad.igv.prefs.PreferencesManager;
 import org.broad.igv.renderer.GraphicUtils;
+import org.broad.igv.renderer.SequenceRenderer;
 import org.broad.igv.sam.AlignmentTrack.ColorOption;
 import org.broad.igv.sam.BisulfiteBaseInfo.DisplayStatus;
 import org.broad.igv.sam.mods.BaseModificationRenderer;
@@ -48,6 +49,8 @@
 import org.broad.igv.ui.color.GreyscaleColorTable;
 import org.broad.igv.ui.color.HSLColorTable;
 import org.broad.igv.ui.color.PaletteColorTable;
+import org.broad.igv.ultima.render.ColorByTagValueList;
+import org.broad.igv.ultima.render.FlowIndelRendering;
 import org.broad.igv.util.ChromosomeColors;
 
 import java.awt.*;
@@ -101,9 +104,9 @@ public class AlignmentRenderer {
 
     // Indel colors
     public static Color purple = new Color(118, 24, 220);
-    private static final Color deletionColor = Color.black;
-    private static final Color skippedColor = new Color(150, 184, 200);
-    private static final Color unknownGapColor = new Color(0, 150, 0);
+    public static Color deletionColor = Color.black;
+    private static Color skippedColor = new Color(150, 184, 200);
+    private static Color unknownGapColor = new Color(0, 150, 0);
 
     // Bisulfite colors
     private static final Color bisulfiteColorFw1 = new Color(195, 195, 195);
@@ -132,6 +135,9 @@ public class AlignmentRenderer {
     private static ColorTable defaultTagColors;
     public static HashMap<Character, Color> nucleotideColors;
 
+    final private static ColorByTagValueList colorByTagValueList = new ColorByTagValueList();
+    final private static FlowIndelRendering flowIndelRendering = new FlowIndelRendering();
+
     private static void initializeTagTypes() {
         // pre-seed from orientation colors
 
@@ -654,9 +660,16 @@ private void drawAlignment(
                             y,
                             h,
                             gapPxEnd - gapPxStart - 2,
+                            context.translateX,
                             null,
+                            alignment,
                             context);
                 }
+
+                // gap extensions
+                if ( flowIndelRendering.handlesAlignment(alignment) ) {
+                    flowIndelRendering.renderDeletionGap(alignment, gap, y, h, gapPxStart, gapPxEnd - gapPxStart, context, renderOptions);
+                }
             }
         }
 
@@ -904,15 +917,21 @@ private void drawAlignment(
                                 y,
                                 h,
                                 (int) pxWidthExact,
+                                context.translateX,
                                 aBlock,
-                                context );
+                                alignment,
+                                context);
                     } else {
                         int pxWing = (h > 10 ? 2 : (h > 5) ? 1 : 0);
                         Graphics2D ig = context.getGraphics();
                         ig.setColor(purple);
-                        ig.fillRect(x, y, 2, h);
-                        ig.fillRect(x - pxWing, y, 2 + 2 * pxWing, 2);
-                        ig.fillRect(x - pxWing, y + h - 2, 2 + 2 * pxWing, 2);
+                        if ( flowIndelRendering.handlesAlignment(alignment) ) {
+                            flowIndelRendering.renderSmallInsertion(alignment, aBlock, context, h, x, y, renderOptions);
+                        } else {
+                            ig.fillRect(x, y, 2, h);
+                            ig.fillRect(x - pxWing, y, 2 + 2 * pxWing, 2);
+                            ig.fillRect(x - pxWing, y + h - 2, 2 + 2 * pxWing, 2);
+                        }
 
                         aBlock.setPixelRange(context.translateX + x - pxWing, context.translateX + x + 2 + pxWing);
                     }
@@ -1018,7 +1037,7 @@ private static void drawClippedEnds(final Graphics2D g, final int[] xPoly, final
     }
 
     private void drawLargeIndelLabel(Graphics2D g, boolean isInsertion, String labelText, int pxCenter,
-                                     int pxTop, int pxH, int pxWmax, AlignmentBlock insertionBlock, RenderContext context) {
+                                     int pxTop, int pxH, int pxWmax, int translateX, AlignmentBlock insertionBlock, Alignment alignment, RenderContext context) {
 
         final int pxPad = 2;   // text padding in the label
         final int pxWing = (pxH > 10 ? 2 : 1);  // width of the cursor "wing"
@@ -1043,8 +1062,12 @@ private void drawLargeIndelLabel(Graphics2D g, boolean isInsertion, String label
         g.fillRect(pxLeft, pxTop, pxRight - pxLeft, pxH);
 
         if (isInsertion && pxH > 5) {
-            g.fillRect(pxLeft - pxWing, pxTop, pxRight - pxLeft + 2 * pxWing, 2);
-            g.fillRect(pxLeft - pxWing, pxTop + pxH - 2, pxRight - pxLeft + 2 * pxWing, 2);
+            if ( flowIndelRendering.handlesAlignment(alignment) ) {
+                flowIndelRendering.renderSmallInsertionWings(alignment, insertionBlock, context, pxH, pxTop, pxRight, pxLeft, track.renderOptions);
+            } else {
+                g.fillRect(pxLeft - pxWing, pxTop, pxRight - pxLeft + 2 * pxWing, 2);
+                g.fillRect(pxLeft - pxWing, pxTop + pxH - 2, pxRight - pxLeft + 2 * pxWing, 2);
+            }
         } // draw "wings" For insertions
 
         if (doesTextFit) {
@@ -1057,6 +1080,104 @@ private void drawLargeIndelLabel(Graphics2D g, boolean isInsertion, String label
         }
     }
 
+    public void renderExpandedInsertion(InsertionMarker i,
+                                        List<Alignment> alignments,
+                                        RenderContext context,
+                                        Rectangle rect,
+                                        boolean leaveMargin) {
+        double origin = context.getOrigin();
+        double locScale = context.getScale();
+        if ((alignments != null) && (alignments.size() > 0)) {
+
+            Graphics2D g = context.getGraphics2D("INSERTIONS");
+            double dX = 1 / context.getScale();
+            int fontSize = (int) Math.min(dX, 12);
+            if (fontSize >= 8) {
+                Font f = FontManager.getFont(Font.BOLD, fontSize);
+                g.setFont(f);
+            }
+
+            for (Alignment alignment : alignments) {
+                if (alignment.getEnd() < i.position) continue;
+                if (alignment.getStart() > i.position) break;
+                AlignmentBlock insertion = alignment.getInsertionAt(i.position);
+                if (insertion != null) {
+
+                    // Compute the start and dend of the alignment in pixels
+                    double pixelStart = (insertion.getStart() - origin) / locScale;
+                    double pixelEnd = (insertion.getEnd() - origin) / locScale;
+                    int x = (int) pixelStart;
+
+                    // If any any part of the feature fits in the track rectangle draw  it
+                    if (pixelEnd < rect.x || pixelStart > rect.getMaxX()) {
+                        continue;
+                    }
+
+                    int bpWidth = insertion.getBasesLength();
+                    double pxWidthExact = ((double) bpWidth) / locScale;
+                    int h = (int) Math.max(1, rect.getHeight() - 2);
+                    int y = (int) (rect.getY() + (rect.getHeight() - h) / 2) - 1;
+
+                    if (!insertion.hasBases()) {
+                        g.setColor(purple);
+                        g.fillRect(x, y, (int) pxWidthExact, h);
+
+                    } else {
+                        drawExpandedInsertionBases(x, context, rect, insertion, leaveMargin);
+                    }
+                }
+            }
+        }
+    }
+
+
+    private void drawExpandedInsertionBases(int pixelPosition,
+                                            RenderContext context,
+                                            Rectangle rect,
+                                            AlignmentBlock block,
+                                            boolean leaveMargin) {
+        Graphics2D g = context.getGraphics2D("INSERTIONS");
+        ByteSubarray bases = block.getBases();
+        int padding = block.getPadding();
+
+        double locScale = context.getScale();
+        double origin = context.getOrigin();
+
+        // Compute bounds
+        int pY = (int) rect.getY();
+        int dY = (int) rect.getHeight();
+        int dX = (int) Math.max(1, (1.0 / locScale));
+
+        final int size = bases.length + padding;
+        for (int p = 0; p < size; p++) {
+
+            char c = p < padding ? '-' : (char) bases.getByte(p - padding);
+
+            Color color = SequenceRenderer.nucleotideColors.get(c);
+            if (color == null) {
+                color = Color.black;
+            }
+
+            // If there is room for text draw the character, otherwise
+            // just draw a rectangle to represent the
+            int pX = (int) (pixelPosition + (p / locScale));
+
+            // Don't draw out of clipping rect
+            if (pX > rect.getMaxX()) {
+                break;
+            } else if (pX + dX < rect.getX()) {
+                continue;
+            }
+            BaseRenderer.drawBase(g, color, c, pX, pY, dX, dY - (leaveMargin ? 2 : 0), false, null);
+        }
+
+        int leftX = pixelPosition + context.translateX;
+        int rightX = leftX + rect.width;
+        block.setPixelRange(leftX, rightX);
+
+    }
+
+
     private Color getAlignmentColor(Alignment alignment, AlignmentTrack track) {
 
         // Set color used to draw the feature.  Highlight features that intersect the
@@ -1205,7 +1326,7 @@ private Color getAlignmentColor(Alignment alignment, AlignmentTrack track) {
             case TAG:
                 final String tag = renderOptions.getColorByTag();
                 if (tag != null) {
-                    Object tagValue = alignment.getAttribute(tag);
+                    Object tagValue = !colorByTagValueList.handlesTag(tag) ? alignment.getAttribute(tag) : colorByTagValueList.getValueForColorByTag(alignment, tag);
                     if (tagValue != null) {
 
                         ColorTable ctable;

src/main/java/org/broad/igv/sam/AlignmentTrack.java

@@ -290,7 +290,7 @@ public static boolean isBisulfiteColorType(ColorOption o) {
     private final Genome genome;
     private ExperimentType experimentType;
     private final AlignmentRenderer renderer;
-    private RenderOptions renderOptions;
+    RenderOptions renderOptions;
 
     private boolean removed = false;
     private boolean showGroupLine;
@@ -1211,6 +1211,7 @@ public static class RenderOptions implements Cloneable, Persistable {
         private Boolean linkedReads;
         private Boolean quickConsensusMode;
         private Boolean showMismatches;
+        private Boolean insertQualColoring;
         Boolean computeIsizes;
         private Double minInsertSizePercentile;
         private Double maxInsertSizePercentile;
@@ -1278,6 +1279,10 @@ public void setViewPairs(boolean viewPairs) {
             this.viewPairs = viewPairs;
         }
 
+        void setInsertQualColoring(boolean insertQualColoring) {
+            this.insertQualColoring = insertQualColoring;
+        }
+
         void setComputeIsizes(boolean computeIsizes) {
             this.computeIsizes = computeIsizes;
         }
@@ -1396,6 +1401,9 @@ public boolean isViewPairs() {
             return viewPairs;
         }
 
+        public boolean isInsertQualColoring() {
+            return insertQualColoring == null ? getPreferences().getAsBoolean(SAM_INSERT_QUAL_COLORING) : insertQualColoring;
+        }
         public boolean isComputeIsizes() {
             return computeIsizes == null ? getPreferences().getAsBoolean(SAM_COMPUTE_ISIZES) : computeIsizes;
         }

src/main/java/org/broad/igv/sam/SAMAlignment.java

@@ -46,6 +46,7 @@
 import org.broad.igv.sam.mods.BaseModificationSet;
 import org.broad.igv.sam.smrt.SMRTKinetics;
 import org.broad.igv.ui.color.ColorUtilities;
+import org.broad.igv.ultima.annotate.FlowBlockAnnotator;
 
 import java.awt.*;
 import java.util.*;
@@ -96,6 +97,8 @@ public class SAMAlignment implements Alignment {
 
     private int flags;
 
+    final private static FlowBlockAnnotator flowBlockAnnotator = new FlowBlockAnnotator();
+
     /**
      * Picard object upon which this SAMAlignment is based
      */
@@ -771,6 +774,10 @@ public String getAlignmentValueString(double position, int mouseX, AlignmentTrac
                             buf.append("Insertion (" + bases.length + " bases): " + new String(bases.copyOfRange(0, 25)) + "..." +
                                     new String(bases.copyOfRange(len - 25, len)) + "<br>");
                         }
+
+                        // extended annotation?
+                        if ( flowBlockAnnotator.handlesBlocks(block) )
+                            flowBlockAnnotator.appendBlockQualityAnnotation(this, block, buf);
                     }
                     atInsertion = true;
                 }
@@ -962,8 +969,10 @@ public String getAlignmentValueString(double position, int mouseX, AlignmentTrac
 
                 byte quality = block.getQuality(offset);
                 buf.append("Location = " + getChr() + ":" + Globals.DECIMAL_FORMAT.format(1 + (long) position) + "<br>");
-                buf.append("Base = " + (char) base + " @ QV " + Globals.DECIMAL_FORMAT.format(quality) + "<br>");
-
+                buf.append("Base = " + (char) base + " @ QV " + Globals.DECIMAL_FORMAT.format(quality));
+                if ( flowBlockAnnotator.handlesBlocks(block) )
+                    flowBlockAnnotator.appendBlockAttrAnnotation(this, block, offset, buf);
+                buf.append("<br>");
                 break;
             }
         }

src/main/java/org/broad/igv/ui/action/LoadFromURLMenuAction.java

@@ -33,11 +33,15 @@
 import org.broad.igv.feature.genome.load.HubGenomeLoader;
 import org.broad.igv.logging.*;
 import org.broad.igv.feature.genome.GenomeManager;
+import org.broad.igv.util.GoogleUtils;
+import org.broad.igv.prefs.Constants;
+import org.broad.igv.prefs.PreferencesManager;
 import org.broad.igv.session.SessionReader;
 import org.broad.igv.ui.IGV;
 import org.broad.igv.ui.util.LoadFromURLDialog;
 import org.broad.igv.ui.util.MessageUtils;
 import org.broad.igv.util.*;
+import org.broad.igv.ui.IGVMenuBar;
 
 import javax.swing.*;
 import java.awt.*;
@@ -205,7 +209,6 @@ private void checkAWSAccessbility(String url) {
                 AmazonUtils.s3ObjectAccessResult res = isObjectAccessible(bucket, key);
                 if (!res.isObjectAvailable()) {
                     MessageUtils.showErrorMessage(res.getErrorReason(), null);
-                    return;
                 }
             }
         } catch (NullPointerException npe) {