From: kiramt <k.mourao@dundee.ac.uk>
Date: Tue, 6 Feb 2018 13:28:54 +0000 (+0000)
Subject: Merge branch 'develop' into feature/JAL-2759
X-Git-Tag: Release_2_10_4~55^2~1^2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=refs%2Fheads%2Ffeature%2FJAL-2759;p=jalview.git

Merge branch 'develop' into feature/JAL-2759

Conflicts:
	benchmarking/README
	src/jalview/datamodel/Alignment.java
	src/jalview/datamodel/AlignmentAnnotation.java
	src/jalview/gui/SeqCanvas.java
	src/jalview/gui/SeqPanel.java
---

8c5cefb3ac80bd094a8dab7ce6735a11583b1772
diff --cc benchmarking/README
index bd2562f,ccf53c1..d1ec146
--- a/benchmarking/README
+++ b/benchmarking/README
@@@ -24,7 -27,14 +27,18 @@@ to install the jalview.jar file in the 
    To get JSON output instead use:
    java -jar target/benchmarks.jar -rf json
    
 +  To run a specific benchmark file use:
 +  java -jar target/benchmarks.jar <Benchmark class name> 
 +  
-   JSON output can be viewed quickly by drag-dropping on http://jmh.morethan.io/
+   JSON output can be viewed quickly by drag-dropping on http://jmh.morethan.io/
+   
+   To get help use the standard -h option:
+   	java -jar target/benchmarks.jar -h
+   	
+   More information here:
+   	http://openjdk.java.net/projects/code-tools/jmh/
+   	http://java-performance.info/jmh/
+   
+   
+  6. If you make changes to the Jalview code everything will need to be refreshed, by performing steps 3-5 again.
++
diff --cc src/jalview/datamodel/Alignment.java
index b6a5e0f,f268d37..9475f00
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@@ -28,7 -28,7 +28,8 @@@ import jalview.util.LinkedIdentityHashS
  import jalview.util.MessageManager;
  
  import java.util.ArrayList;
+ import java.util.Arrays;
 +import java.util.BitSet;
  import java.util.Collections;
  import java.util.Enumeration;
  import java.util.HashSet;
diff --cc src/jalview/datamodel/AlignmentAnnotation.java
index 6c33c1b,f7bf4d8..0098d76
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@@ -1473,113 -1473,70 +1473,179 @@@ public class AlignmentAnnotatio
      return graphMin < graphMax;
    }
  
 +  /**
 +   * delete any columns in alignmentAnnotation that are hidden (including
 +   * sequence associated annotation).
 +   * 
 +   * @param hiddenColumns
 +   *          the set of hidden columns
 +   */
 +  public void makeVisibleAnnotation(HiddenColumns hiddenColumns)
 +  {
 +    if (annotations != null)
 +    {
 +      makeVisibleAnnotation(0, annotations.length, hiddenColumns);
 +    }
 +  }
 +
 +  /**
 +   * delete any columns in alignmentAnnotation that are hidden (including
 +   * sequence associated annotation).
 +   * 
 +   * @param start
 +   *          remove any annotation to the right of this column
 +   * @param end
 +   *          remove any annotation to the left of this column
 +   * @param hiddenColumns
 +   *          the set of hidden columns
 +   */
 +  public void makeVisibleAnnotation(int start, int end,
 +          HiddenColumns hiddenColumns)
 +  {
 +    if (annotations != null)
 +    {
 +      if (hiddenColumns.hasHiddenColumns())
 +      {
 +        removeHiddenAnnotation(start, end, hiddenColumns);
 +      }
 +      else
 +      {
 +        restrict(start, end);
 +      }
 +    }
 +  }
 +
 +  /**
 +   * The actual implementation of deleting hidden annotation columns
 +   * 
 +   * @param start
 +   *          remove any annotation to the right of this column
 +   * @param end
 +   *          remove any annotation to the left of this column
 +   * @param hiddenColumns
 +   *          the set of hidden columns
 +   */
 +  private void removeHiddenAnnotation(int start, int end,
 +          HiddenColumns hiddenColumns)
 +  {
 +    // mangle the alignmentAnnotation annotation array
 +    ArrayList<Annotation[]> annels = new ArrayList<>();
 +    Annotation[] els = null;
 +
 +    int w = 0;
 +
 +    Iterator<int[]> blocks = hiddenColumns.getVisContigsIterator(start,
 +            end + 1, false);
 +
 +    int copylength;
 +    int annotationLength;
 +    while (blocks.hasNext())
 +    {
 +      int[] block = blocks.next();
 +      annotationLength = block[1] - block[0] + 1;
 +
 +      if (blocks.hasNext())
 +      {
 +        // copy just the visible segment of the annotation row
 +        copylength = annotationLength;
 +      }
 +      else
 +      {
 +        if (annotationLength + block[0] <= annotations.length)
 +        {
 +          // copy just the visible segment of the annotation row
 +          copylength = annotationLength;
 +        }
 +        else
 +        {
 +          // copy to the end of the annotation row
 +          copylength = annotations.length - block[0];
 +        }
 +      }
 +
 +      els = new Annotation[annotationLength];
 +      annels.add(els);
 +      System.arraycopy(annotations, block[0], els, 0, copylength);
 +      w += annotationLength;
 +    }
 +
 +    if (w != 0)
 +    {
 +      annotations = new Annotation[w];
 +
 +      w = 0;
 +      for (Annotation[] chnk : annels)
 +      {
 +        System.arraycopy(chnk, 0, annotations, w, chnk.length);
 +        w += chnk.length;
 +      }
 +    }
 +  }
 +
+   public static Iterable<AlignmentAnnotation> findAnnotations(
+           Iterable<AlignmentAnnotation> list, SequenceI seq, String calcId,
+           String label)
+   {
+ 
+     ArrayList<AlignmentAnnotation> aa = new ArrayList<>();
+     for (AlignmentAnnotation ann : list)
+     {
+       if ((calcId == null || (ann.getCalcId() != null
+               && ann.getCalcId().equals(calcId)))
+               && (seq == null || (ann.sequenceRef != null
+                       && ann.sequenceRef == seq))
+               && (label == null
+                       || (ann.label != null && ann.label.equals(label))))
+       {
+         aa.add(ann);
+       }
+     }
+     return aa;
+   }
+ 
+   /**
+    * Answer true if any annotation matches the calcId passed in (if not null).
+    * 
+    * @param list
+    *          annotation to search
+    * @param calcId
+    * @return
+    */
+   public static boolean hasAnnotation(List<AlignmentAnnotation> list,
+           String calcId)
+   {
+ 
+     if (calcId != null && !"".equals(calcId))
+     {
+       for (AlignmentAnnotation a : list)
+       {
+         if (a.getCalcId() == calcId)
+         {
+           return true;
+         }
+       }
+     }
+     return false;
+   }
+ 
+   public static Iterable<AlignmentAnnotation> findAnnotation(
+           List<AlignmentAnnotation> list, String calcId)
+   {
+ 
+     List<AlignmentAnnotation> aa = new ArrayList<>();
+     if (calcId == null)
+     {
+       return aa;
+     }
+     for (AlignmentAnnotation a : list)
+     {
+ 
+       if (a.getCalcId() == calcId || (a.getCalcId() != null
+               && calcId != null && a.getCalcId().equals(calcId)))
+       {
+         aa.add(a);
+       }
+     }
+     return aa;
+   }
  }
diff --cc src/jalview/gui/SeqCanvas.java
index cdf84b7,1e1105f..fb81f4d
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@@ -1775,12 -1799,27 +1775,19 @@@ public class SeqCanvas extends JCompone
          {
            fastPaint(scrollX, 0);
          }
-         // bizarrely, we only need to scroll on the x value here as fastpaint
-         // copies the full height of the image anyway. Passing in the y value
-         // causes nasty repaint artefacts, which only disappear on a full
-         // repaint.
+     }
+     else if (eventName.equals(ViewportRanges.STARTSEQ))
+     {
+       // scroll
+       fastPaint(0, (int) evt.getNewValue() - (int) evt.getOldValue());
+     }
+     else if (eventName.equals(ViewportRanges.STARTRESANDSEQ))
+     {
+       if (av.getWrapAlignment())
+       {
+         fastPaintWrapped(scrollX);
        }
-     
 -      else
 -      {
 -        fastPaint(scrollX, 0);
 -      }
 -      // bizarrely, we only need to scroll on the x value here as fastpaint
 -      // copies the full height of the image anyway. Passing in the y value
 -      // causes nasty repaint artefacts, which only disappear on a full
 -      // repaint.
+     }
    }
  
    /**
diff --cc src/jalview/gui/SeqPanel.java
index 9359569,61cac46..84b85e9
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@@ -434,7 -422,10 +434,10 @@@ public class SeqPanel extends JPane
      {
        if (av.getWrapAlignment())
        {
-         av.getRanges().scrollToWrappedVisible(seqCanvas.cursorX);
+         // scrollToWrappedVisible expects x-value to have hidden cols subtracted
+         int x = av.getAlignment().getHiddenColumns()
 -                .findColumnPosition(seqCanvas.cursorX);
++                .absoluteToVisibleColumn(seqCanvas.cursorX);
+         av.getRanges().scrollToWrappedVisible(x);
        }
        else
        {
diff --cc src/jalview/renderer/AnnotationRenderer.java
index 25a81f9,8a80d41..adca17e
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@@ -162,7 -162,8 +162,8 @@@ public class AnnotationRendere
            boolean validRes, boolean validEnd)
    {
      g.setColor(STEM_COLOUR);
-     int sCol = (lastSSX / charWidth) + startRes;
+     int sCol = (lastSSX / charWidth)
 -            + hiddenColumns.adjustForHiddenColumns(startRes);
++            + hiddenColumns.visibleToAbsoluteColumn(startRes);
      int x1 = lastSSX;
      int x2 = (x * charWidth);
  
@@@ -228,7 -229,8 +229,8 @@@
      // System.out.println(nonCanColor);
  
      g.setColor(nonCanColor);
-     int sCol = (lastSSX / charWidth) + startRes;
+     int sCol = (lastSSX / charWidth)
 -            + hiddenColumns.adjustForHiddenColumns(startRes);
++            + hiddenColumns.visibleToAbsoluteColumn(startRes);
      int x1 = lastSSX;
      int x2 = (x * charWidth);
  
@@@ -1147,7 -1149,8 +1149,8 @@@
    {
      g.setColor(HELIX_COLOUR);
  
-     int sCol = (lastSSX / charWidth) + startRes;
+     int sCol = (lastSSX / charWidth)
 -            + hiddenColumns.adjustForHiddenColumns(startRes);
++            + hiddenColumns.visibleToAbsoluteColumn(startRes);
      int x1 = lastSSX;
      int x2 = (x * charWidth);