(JAL-811) new 'annotation type' field for marking annotation rows generated by alignm...

[jalview.git] / src / jalview / gui / AlignmentPanel.java

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index d2aa6d6..bfbaf4d 100644 (file)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -32,7 +32,6 @@ import jalview.bin.Cache;
 import jalview.datamodel.*;
 import jalview.jbgui.*;
 import jalview.schemes.*;
-import jalview.structure.SelectionSource;
 import jalview.structure.StructureSelectionManager;
 
 /**
@@ -263,16 +262,16 @@ public class AlignmentPanel extends GAlignmentPanel implements
     // do we need to scroll the panel?
     // TODO: tons of nullpointereexceptions raised here.
     if (results != null && results.getSize() > 0 && av != null
-            && av.alignment != null)
+            && av.getAlignment() != null)
     {
-      int seqIndex = av.alignment.findIndex(results);
+      int seqIndex = av.getAlignment().findIndex(results);
       if (seqIndex == -1)
       {
         return false;
       }
-      SequenceI seq = av.alignment.getSequenceAt(seqIndex);
+      SequenceI seq = av.getAlignment().getSequenceAt(seqIndex);
       
-      int[] r=results.getResults(seq, 0, av.alignment.getWidth());
+      int[] r=results.getResults(seq, 0, av.getAlignment().getWidth());
       if (r == null)
       {
         return false;
@@ -289,13 +288,13 @@ public class AlignmentPanel extends GAlignmentPanel implements
       {
         return false;
       }
-      if (av.hasHiddenColumns)
+      if (av.hasHiddenColumns())
       {
         start = av.getColumnSelection().findColumnPosition(start);
         end = av.getColumnSelection().findColumnPosition(end);
         if (start==end)
         {
-          if (!av.colSel.isVisible(r[0]))
+          if (!av.getColumnSelection().isVisible(r[0]))
           {
             // don't scroll - position isn't visible
             return false;
@@ -396,7 +395,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     }
     validateAnnotationDimensions(true);
     addNotify();
-    repaint();
+    paintAlignment(true);
   }
   /**
    * calculate the annotation dimensions and refresh slider values accordingly.
@@ -534,14 +533,14 @@ public class AlignmentPanel extends GAlignmentPanel implements
   public void setScrollValues(int x, int y)
   {
     // System.err.println("Scroll to "+x+","+y);
-    if (av == null || av.alignment == null)
+    if (av == null || av.getAlignment() == null)
     {
       return;
     }
-    int width = av.alignment.getWidth();
-    int height = av.alignment.getHeight();
+    int width = av.getAlignment().getWidth();
+    int height = av.getAlignment().getHeight();
 
-    if (av.hasHiddenColumns)
+    if (av.hasHiddenColumns())
     {
       width = av.getColumnSelection().findColumnPosition(width);
     }
@@ -710,9 +709,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     if (av.getWrapAlignment())
     {
-      int maxwidth = av.alignment.getWidth();
+      int maxwidth = av.getAlignment().getWidth();
 
-      if (av.hasHiddenColumns)
+      if (av.hasHiddenColumns())
       {
         maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
       }
@@ -836,7 +835,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
       endSeq = av.getAlignment().getHeight();
     }
 
-    int pagesHigh = ((av.alignment.getHeight() / totalSeq) + 1) * pheight;
+    int pagesHigh = ((av.getAlignment().getHeight() / totalSeq) + 1) * pheight;
 
     if (av.showAnnotation)
     {
@@ -907,12 +906,12 @@ public class AlignmentPanel extends GAlignmentPanel implements
     pg.translate(idWidth, 0);
     seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq, 0);
 
-    if (av.showAnnotation && (endSeq == av.alignment.getHeight()))
+    if (av.showAnnotation && (endSeq == av.getAlignment().getHeight()))
     {
       pg.translate(-idWidth - 3, (endSeq - startSeq) * av.charHeight + 3);
       alabels.drawComponent((Graphics2D) pg, idWidth);
       pg.translate(idWidth + 3, 0);
-      annotationPanel.drawComponent((Graphics2D) pg, startRes, endRes + 1);
+      annotationPanel.renderer.drawComponent(annotationPanel, av, (Graphics2D) pg, -1, startRes, endRes + 1);
     }
 
     return Printable.PAGE_EXISTS;
@@ -958,8 +957,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     int idWidth = getVisibleIdWidth();
 
-    int maxwidth = av.alignment.getWidth();
-    if (av.hasHiddenColumns)
+    int maxwidth = av.getAlignment().getWidth();
+    if (av.hasHiddenColumns())
     {
       maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
     }
@@ -985,10 +984,10 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     do
     {
-      for (int i = 0; i < av.alignment.getHeight(); i++)
+      for (int i = 0; i < av.getAlignment().getHeight(); i++)
       {
         pg.setFont(idPanel.idCanvas.idfont);
-        SequenceI s = av.alignment.getSequenceAt(i);
+        SequenceI s = av.getAlignment().getSequenceAt(i);
         String string = s.getDisplayId(av.getShowJVSuffix());
         int xPos = 0;
         if (av.rightAlignIds)
@@ -1038,13 +1037,13 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
   void makeAlignmentImage(int type, File file)
   {
-    int maxwidth = av.alignment.getWidth();
-    if (av.hasHiddenColumns)
+    int maxwidth = av.getAlignment().getWidth();
+    if (av.hasHiddenColumns())
     {
       maxwidth = av.getColumnSelection().findColumnPosition(maxwidth);
     }
 
-    int height = ((av.alignment.getHeight() + 1) * av.charHeight)
+    int height = ((av.getAlignment().getHeight() + 1) * av.charHeight)
             + scalePanel.getHeight();
     int width = getVisibleIdWidth() + (maxwidth * av.charWidth);
 
@@ -1146,7 +1145,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     {
       try
       {
-        int s, sSize = av.alignment.getHeight(), res, alwidth = av.alignment
+        int s, sSize = av.getAlignment().getHeight(), res, alwidth = av.getAlignment()
                 .getWidth(), g, gSize, f, fSize, sy;
         StringBuffer text = new StringBuffer();
         PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
@@ -1159,15 +1158,15 @@ public class AlignmentPanel extends GAlignmentPanel implements
         {
           sy = s * av.charHeight + scaleHeight;
 
-          SequenceI seq = av.alignment.getSequenceAt(s);
+          SequenceI seq = av.getAlignment().getSequenceAt(s);
           SequenceFeature[] features = seq.getDatasetSequence()
                   .getSequenceFeatures();
-          SequenceGroup[] groups = av.alignment.findAllGroups(seq);
+          SequenceGroup[] groups = av.getAlignment().findAllGroups(seq);
           for (res = 0; res < alwidth; res++)
           {
             text = new StringBuffer();
             Object obj = null;
-            if (av.alignment.isNucleotide())
+            if (av.getAlignment().isNucleotide())
             {
               obj = ResidueProperties.nucleotideName.get(seq.getCharAt(res)
                       + "");
@@ -1303,8 +1302,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
     int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap
             + annotationHeight;
 
-    int maxwidth = av.alignment.getWidth();
-    if (av.hasHiddenColumns)
+    int maxwidth = av.getAlignment().getWidth();
+    if (av.hasHiddenColumns())
     {
       maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
     }
@@ -1328,7 +1327,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
       jalview.structure.StructureSelectionManager ssm = av.getStructureSelectionManager();
       ssm.removeStructureViewerListener(seqPanel, null);
       ssm.removeSelectionListener(seqPanel);
-      av.alignment = null;
+      av.setAlignment(null);
       av = null;
     }
     else
@@ -1357,16 +1356,17 @@ public class AlignmentPanel extends GAlignmentPanel implements
     boolean cons = av.isShowGroupConsensus();
     boolean showprf = av.isShowSequenceLogo();
     boolean showConsHist = av.isShowConsensusHistogram();
+    boolean normLogo = av.isNormaliseSequenceLogo();
 
     boolean sortg = true;
 
     // remove old automatic annotation
     // add any new annotation
 
-    Vector gr = av.alignment.getGroups(); // OrderedBy(av.alignment.getSequencesArray());
+    Vector gr = av.getAlignment().getGroups(); // OrderedBy(av.getAlignment().getSequencesArray());
     // intersect alignment annotation with alignment groups
 
-    AlignmentAnnotation[] aan = av.alignment.getAlignmentAnnotation();
+    AlignmentAnnotation[] aan = av.getAlignment().getAlignmentAnnotation();
     Hashtable oldrfs = new Hashtable();
     if (aan != null)
     {
@@ -1375,7 +1375,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
         if (aan[an].autoCalculated && aan[an].groupRef != null)
         {
           oldrfs.put(aan[an].groupRef, aan[an].groupRef);
-          av.alignment.deleteAnnotation(aan[an]);
+          av.getAlignment().deleteAnnotation(aan[an]);
           aan[an] = null;
         }
       }
@@ -1392,16 +1392,17 @@ public class AlignmentPanel extends GAlignmentPanel implements
           // set defaults for this group's conservation/consensus
           sg.setshowSequenceLogo(showprf);
           sg.setShowConsensusHistogram(showConsHist);
+          sg.setNormaliseSequenceLogo(normLogo);
         }
         if (conv)
         {
           updateCalcs = true;
-          av.alignment.addAnnotation(sg.getConservationRow(), 0);
+          av.getAlignment().addAnnotation(sg.getConservationRow(), 0);
         }
         if (cons)
         {
           updateCalcs = true;
-          av.alignment.addAnnotation(sg.getConsensus(), 0);
+          av.getAlignment().addAnnotation(sg.getConsensus(), 0);
         }
         // refresh the annotation rows
         if (updateCalcs)
@@ -1417,7 +1418,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
   @Override
   public AlignmentI getAlignment()
   {
-    return av.alignment;
+    return av.getAlignment();
   }
 
   /**
@@ -1450,4 +1451,10 @@ public class AlignmentPanel extends GAlignmentPanel implements
   {
     return av.getStructureSelectionManager();
   }
+
+  @Override
+  public void raiseOOMWarning(String string, OutOfMemoryError error)
+  {
+    new OOMWarning(string,  error, this);
+  }
 }