X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=b68008a0495a467e946fcd83b38e05ba11fb0052;hb=5c57814f95e73a63e012479651b919fdc4099f53;hp=fb2047ebcd2b1c5b0e60aa5b7f08a91c1eff8db0;hpb=2947e06daee7e5b9d76be0d817dc45f0c8e94400;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index fb2047e..b68008a 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -1,6 +1,6 @@
  /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -18,6 +18,10 @@
  */
 package jalview.gui;
 
+import java.util.*;
+
+import java.awt.*;
+
 import jalview.analysis.*;
 
 import jalview.bin.*;
@@ -26,11 +30,6 @@ import jalview.datamodel.*;
 
 import jalview.schemes.*;
 
-import java.awt.*;
-
-import java.util.*;
-
-
 /**
  * DOCUMENT ME!
  *
@@ -61,6 +60,7 @@ public class AlignViewport
     boolean validCharWidth;
     int wrappedWidth;
     Font font;
+    boolean seqNameItalics;
     AlignmentI alignment;
     ColumnSelection colSel = new ColumnSelection();
     int threshold;
@@ -91,7 +91,8 @@ public class AlignViewport
     public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
 
     // JBPNote Prolly only need this in the applet version.
-    private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(this);
+  private java.beans.PropertyChangeSupport changeSupport = new java.beans.
+      PropertyChangeSupport(this);
 
     boolean ignoreGapsInConsensusCalculation = false;
 
@@ -120,6 +121,8 @@ public class AlignViewport
 
     boolean rightAlignIds = false;
 
+    Hashtable hiddenRepSequences;
+
 
     /**
      * Creates a new AlignViewport object.
@@ -136,13 +139,17 @@ public class AlignViewport
      * @param al AlignmentI
      * @param hiddenColumns ColumnSelection
      */
-    public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns) {
+  public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns)
+  {
       setAlignment(al);
-      if (hiddenColumns!=null) {
+    if (hiddenColumns != null)
+    {
         this.colSel = hiddenColumns;
         if (hiddenColumns.getHiddenColumns() != null)
+      {
           hasHiddenColumns = true;
       }
+    }
       init();
     }
 
@@ -168,6 +175,8 @@ public class AlignViewport
        String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "") ;
        String fontSize = Cache.getDefault("FONT_SIZE", "10");
 
+       seqNameItalics = Cache.getDefault("ID_ITALICS", true);
+
        int style = 0;
 
        if (fontStyle.equals("bold"))
@@ -197,6 +206,7 @@ public class AlignViewport
                 11f,
                 AlignmentAnnotation.BAR_GRAPH);
             conservation.hasText = true;
+            conservation.autoCalculated=true;
 
 
             if (Cache.getDefault("SHOW_CONSERVATION", true))
@@ -213,6 +223,7 @@ public class AlignViewport
                                                 11f,
                                                 AlignmentAnnotation.BAR_GRAPH);
               quality.hasText = true;
+              quality.autoCalculated=true;
 
               alignment.addAnnotation(quality);
             }
@@ -222,6 +233,7 @@ public class AlignViewport
                                                new Annotation[1], 0f, 100f,
                                                AlignmentAnnotation.BAR_GRAPH);
           consensus.hasText = true;
+          consensus.autoCalculated=true;
 
            if (Cache.getDefault("SHOW_IDENTITY", true))
            {
@@ -237,7 +249,8 @@ public class AlignViewport
             if (globalColourScheme instanceof UserColourScheme)
             {
                 globalColourScheme = UserDefinedColours.loadDefaultColours();
-                ((UserColourScheme)globalColourScheme).setThreshold(0, getIgnoreGapsConsensus());
+        ( (UserColourScheme) globalColourScheme).setThreshold(0,
+            getIgnoreGapsConsensus());
             }
 
             if (globalColourScheme != null)
@@ -266,9 +279,8 @@ public class AlignViewport
       return showSequenceFeatures;
     }
 
-
-
-    class ConservationThread extends Thread
+  class ConservationThread
+      extends Thread
     {
       AlignmentPanel ap;
       public ConservationThread(AlignmentPanel ap)
@@ -288,7 +300,7 @@ public class AlignViewport
             {
               if (ap != null)
               {
-                ap.repaint();
+              ap.paintAlignment(true);
               }
               Thread.sleep(200);
             }
@@ -303,7 +315,9 @@ public class AlignViewport
 
           int alWidth = alignment.getWidth();
           if(alWidth<0)
+        {
             return;
+        }
 
           Conservation cons = new jalview.analysis.Conservation("All",
               jalview.schemes.ResidueProperties.propHash, 3,
@@ -317,7 +331,7 @@ public class AlignViewport
             cons.findQuality();
           }
 
-          String sequence = cons.getConsSequence().getSequence();
+          char [] sequence = cons.getConsSequence().getSequence();
           float minR;
           float minG;
           float minB;
@@ -352,14 +366,20 @@ public class AlignViewport
           {
             float value = 0;
 
-            c = sequence.charAt(i);
+            c = sequence[i];
 
             if (Character.isDigit(c))
+          {
               value = (int) (c - '0');
+          }
             else if (c == '*')
+          {
               value = 11;
+          }
             else if (c == '+')
+          {
               value = 10;
+          }
 
             float vprop = value - min;
             vprop /= max;
@@ -376,7 +396,8 @@ public class AlignViewport
               value = ( (Double) cons.quality.get(i)).floatValue();
               vprop = value - qmin;
               vprop /= qmax;
-              quality.annotations[i] = new Annotation(" ", String.valueOf(value), ' ',
+            quality.annotations[i] = new Annotation(" ", String.valueOf(value),
+                ' ',
                                                value,
                                                new Color(minR + (maxR * vprop),
                   minG + (maxG * vprop),
@@ -414,7 +435,7 @@ public class AlignViewport
 
         if(ap!=null)
         {
-          ap.repaint();
+        ap.paintAlignment(true);
         }
 
       }
@@ -441,7 +462,9 @@ public class AlignViewport
     public void updateConservation(final AlignmentPanel ap)
     {
       if (alignment.isNucleotide() || conservation==null)
+    {
         return;
+    }
 
       conservationThread = new ConservationThread(ap);
       conservationThread.start();
@@ -456,8 +479,8 @@ public class AlignViewport
       consensusThread.start();
     }
 
-
-    class ConsensusThread extends Thread
+  class ConsensusThread
+      extends Thread
     {
       AlignmentPanel ap;
       public ConsensusThread(AlignmentPanel ap)
@@ -473,7 +496,7 @@ public class AlignViewport
           {
             if (ap != null)
             {
-              ap.repaint();
+            ap.paintAlignment(true);
             }
 
             Thread.sleep(200);
@@ -491,7 +514,9 @@ public class AlignViewport
         {
           int aWidth = alignment.getWidth();
           if(aWidth<0)
+        {
             return;
+        }
 
           consensus.annotations = null;
           consensus.annotations = new Annotation[aWidth];
@@ -507,11 +532,15 @@ public class AlignViewport
           {
             float value = 0;
             if (ignoreGapsInConsensusCalculation)
+          {
               value = ( (Float) hconsensus[i].get(AAFrequency.PID_NOGAPS)).
                   floatValue();
+          }
             else
+          {
               value = ( (Float) hconsensus[i].get(AAFrequency.PID_GAPS)).
                   floatValue();
+          }
 
             String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE).toString();
             String mouseOver = hconsensus[i].get(AAFrequency.MAXRESIDUE) + " ";
@@ -523,12 +552,15 @@ public class AlignViewport
             }
 
             mouseOver += ( (int) value + "%");
-            consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);
+          consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ',
+              value);
           }
 
 
           if (globalColourScheme != null)
+        {
             globalColourScheme.setConsensus(hconsensus);
+        }
 
         }
         catch (OutOfMemoryError error)
@@ -558,7 +590,7 @@ public class AlignViewport
 
         if (ap != null)
         {
-          ap.repaint();
+        ap.paintAlignment(true);
         }
       }
     }
@@ -566,23 +598,36 @@ public class AlignViewport
      * get the consensus sequence as displayed under the PID consensus annotation row.
      * @return consensus sequence as a new sequence object
      */
-    public SequenceI getConsensusSeq() {
+  public SequenceI getConsensusSeq()
+  {
       if (consensus==null)
+    {
         updateConsensus(null);
+    }
       if (consensus==null)
+    {
         return null;
+    }
       StringBuffer seqs=new StringBuffer();
-      for (int i=0; i<consensus.annotations.length; i++) {
-        if (consensus.annotations[i]!=null) {
+    for (int i = 0; i < consensus.annotations.length; i++)
+    {
+      if (consensus.annotations[i] != null)
+      {
           if (consensus.annotations[i].description.charAt(0) == '[')
+        {
             seqs.append(consensus.annotations[i].description.charAt(1));
+        }
           else
+        {
             seqs.append(consensus.annotations[i].displayCharacter);
         }
       }
+    }
 
       SequenceI sq = new Sequence("Consensus", seqs.toString());
-      sq.setDescription("Percentage Identity Consensus "+((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
+    sq.setDescription("Percentage Identity Consensus " +
+                      ( (ignoreGapsInConsensusCalculation) ? " without gaps" :
+                       ""));
       return sq;
     }
     /**
@@ -1220,7 +1265,8 @@ public class AlignViewport
       updateConsensus(ap);
       if(globalColourScheme!=null)
       {
-        globalColourScheme.setThreshold(globalColourScheme.getThreshold(), ignoreGapsInConsensusCalculation);
+      globalColourScheme.setThreshold(globalColourScheme.getThreshold(),
+                                      ignoreGapsInConsensusCalculation);
       }
     }
 
@@ -1243,7 +1289,9 @@ public class AlignViewport
     public void hideSelectedColumns()
     {
       if (colSel.size() < 1)
+    {
         return;
+    }
 
       colSel.hideSelectedColumns();
       setSelectionGroup(null);
@@ -1255,17 +1303,58 @@ public class AlignViewport
     public void hideColumns(int start, int end)
     {
       if(start==end)
+    {
         colSel.hideColumns(start);
+    }
       else
+    {
         colSel.hideColumns(start, end);
+    }
 
       hasHiddenColumns = true;
     }
 
+    public void hideRepSequences(SequenceI repSequence, SequenceGroup sg)
+    {
+      int sSize = sg.getSize();
+      if(sSize < 2)
+    {
+        return;
+    }
+
+      if(hiddenRepSequences==null)
+    {
+        hiddenRepSequences = new Hashtable();
+    }
+
+       hiddenRepSequences.put(repSequence, sg);
+
+      //Hide all sequences except the repSequence
+      SequenceI [] seqs = new SequenceI[sSize-1];
+      int index = 0;
+      for(int i=0; i<sSize; i++)
+    {
+        if(sg.getSequenceAt(i)!=repSequence)
+        {
+          if(index==sSize-1)
+        {
+            return;
+        }
+
+          seqs[index++] = sg.getSequenceAt(i);
+        }
+    }
+
+      hideSequence(seqs);
+
+    }
+
     public void hideAllSelectedSeqs()
     {
-      if (selectionGroup == null)
+    if (selectionGroup == null || selectionGroup.getSize()<1)
+    {
         return;
+    }
 
       SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment);
 
@@ -1279,8 +1368,9 @@ public class AlignViewport
       if(seq!=null)
       {
         for (int i = 0; i < seq.length; i++)
+        {
           alignment.getHiddenSequences().hideSequence(seq[i]);
-
+        }
         hasHiddenRows = true;
         firePropertyChange("alignment", null, alignment.getSequences());
       }
@@ -1288,7 +1378,8 @@ public class AlignViewport
 
     public void showSequence(int index)
     {
-      Vector tmp = alignment.getHiddenSequences().showSequence(index);
+      Vector tmp = alignment.getHiddenSequences().showSequence(index
+          , hiddenRepSequences);
       if(tmp.size()>0)
       {
         if(selectionGroup==null)
@@ -1307,15 +1398,19 @@ public class AlignViewport
       }
 
       if(alignment.getHiddenSequences().getSize()<1)
+    {
         hasHiddenRows = false;
     }
+  }
 
     public void showColumn(int col)
     {
       colSel.revealHiddenColumns(col);
       if(colSel.getHiddenColumns()==null)
+    {
         hasHiddenColumns = false;
     }
+  }
 
     public void showAllHiddenColumns()
     {
@@ -1332,7 +1427,7 @@ public class AlignViewport
           selectionGroup = new SequenceGroup();
           selectionGroup.setEndRes(alignment.getWidth()-1);
         }
-        Vector tmp = alignment.getHiddenSequences().showAll();
+        Vector tmp = alignment.getHiddenSequences().showAll(hiddenRepSequences);
         for(int t=0; t<tmp.size(); t++)
         {
           selectionGroup.addSequence(
@@ -1341,15 +1436,20 @@ public class AlignViewport
         }
         firePropertyChange("alignment", null, alignment.getSequences());
         hasHiddenRows = false;
+        hiddenRepSequences = null;
       }
     }
 
+
+
     public void invertColumnSelection()
     {
       for(int i=0; i<alignment.getWidth(); i++)
       {
         if(colSel.contains(i))
+      {
           colSel.removeElement(i);
+      }
         else
         {
           if (!hasHiddenColumns || colSel.isVisible(i))
@@ -1357,9 +1457,7 @@ public class AlignViewport
             colSel.addElement(i);
           }
         }
-
       }
-
     }
 
     public int adjustForHiddenSeqs(int alignmentIndex)
@@ -1368,8 +1466,10 @@ public class AlignViewport
     }
 
     /**
-     * This method returns the a new SequenceI [] with
-     * the selection sequence and start and end points adjusted
+     * This method returns an array of new SequenceI objects 
+     * derived from the whole alignment or just the current
+     * selection with start and end points adjusted
+     * @note if you need references to the actual SequenceI objects in the alignment or currently selected then use getSequenceSelection()
      * @return String[]
      */
     public SequenceI[] getSelectionAsNewSequence()
@@ -1377,13 +1477,38 @@ public class AlignViewport
       SequenceI[] sequences;
 
       if (selectionGroup == null)
+    {
         sequences = alignment.getSequencesArray();
+        AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation(); 
+        for (int i=0; i<sequences.length; i++)
+        {
+          sequences[i] = new Sequence(sequences[i], annots); // construct new sequence with subset of visible annotation
+        }
+    }
       else
+    {
         sequences = selectionGroup.getSelectionAsNewSequences(alignment);
+    }
 
       return sequences;
     }
-
+    /**
+     * get the currently selected sequence objects or all the sequences in the alignment.
+     * @return array of references to sequence objects
+     */
+    public SequenceI[] getSequenceSelection()
+    {
+      SequenceI[] sequences;
+      if (selectionGroup==null)
+      {
+        sequences = alignment.getSequencesArray();
+      }
+      else
+      {
+        sequences = selectionGroup.getSequencesInOrder(alignment);
+      }
+      return sequences;
+    }
     /**
      * This method returns the visible alignment as text, as
      * seen on the GUI, ie if columns are hidden they will not
@@ -1392,7 +1517,8 @@ public class AlignViewport
      * which contain hidden columns.
      * @return String[]
      */
-    public jalview.datamodel.CigarArray getViewAsCigars(boolean selectedRegionOnly)
+  public jalview.datamodel.CigarArray getViewAsCigars(boolean
+      selectedRegionOnly)
     {
       CigarArray selection=null;
       SequenceI [] seqs= null;
@@ -1400,7 +1526,7 @@ public class AlignViewport
       int start = 0, end = 0;
       if(selectedRegionOnly && selectionGroup!=null)
       {
-        iSize = selectionGroup.getSize(false);
+        iSize = selectionGroup.getSize();
         seqs = selectionGroup.getSequencesInOrder(alignment);
         start = selectionGroup.getStartRes();
         end = selectionGroup.getEndRes(); // inclusive for start and end in SeqCigar constructor
@@ -1418,7 +1544,8 @@ public class AlignViewport
       }
       selection=new CigarArray(selseqs);
       // now construct the CigarArray operations
-      if (hasHiddenColumns) {
+    if (hasHiddenColumns)
+    {
         Vector regions = colSel.getHiddenColumns();
         int [] region;
         int hideStart, hideEnd;
@@ -1429,34 +1556,50 @@ public class AlignViewport
           hideStart = region[0];
           hideEnd = region[1];
           // edit hidden regions to selection range
-          if(hideStart<last) {
+        if (hideStart < last)
+        {
             if (hideEnd > last)
             {
               hideStart = last;
-            } else
+          }
+          else
+          {
               continue;
           }
+        }
 
           if (hideStart>end)
+        {
             break;
+        }
 
           if (hideEnd>end)
+        {
             hideEnd=end;
+        }
 
           if (hideStart>hideEnd)
+        {
             break;
+        }
           /**
            * form operations...
            */
           if (last<hideStart)
+        {
             selection.addOperation(CigarArray.M, hideStart-last);
+        }
           selection.addOperation(CigarArray.D, 1+hideEnd-hideStart);
           last = hideEnd+1;
         }
         // Final match if necessary.
         if (last<end)
+      {
           selection.addOperation(CigarArray.M, end-last+1);
-      } else {
+      }
+    }
+    else
+    {
         selection.addOperation(CigarArray.M, end-start+1);
       }
       return selection;
@@ -1467,15 +1610,18 @@ public class AlignViewport
      * @param selectedOnly boolean true to just return the selected view
      * @return AlignmentView
      */
-    jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly) {
+  jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly)
+  {
       // JBPNote:
       // this is here because the AlignmentView constructor modifies the CigarArray
       // object. Refactoring of Cigar and alignment view representation should
       // be done to remove redundancy.
       CigarArray aligview = getViewAsCigars(selectedOnly);
-      if (aligview!=null) {
+    if (aligview != null)
+    {
         return new AlignmentView(aligview,
-            (selectedOnly && selectionGroup!=null) ? selectionGroup.getStartRes() : 0);
+                               (selectedOnly && selectionGroup != null) ?
+                               selectionGroup.getStartRes() : 0);
       }
       return null;
     }
@@ -1495,7 +1641,7 @@ public class AlignViewport
       int start = 0, end = 0;
       if(selectedRegionOnly && selectionGroup!=null)
       {
-        iSize = selectionGroup.getSize(false);
+        iSize = selectionGroup.getSize();
         seqs = selectionGroup.getSequencesInOrder(alignment);
         start = selectionGroup.getStartRes();
         end = selectionGroup.getEndRes()+1;
@@ -1508,18 +1654,66 @@ public class AlignViewport
       }
 
       selection = new String[iSize];
-      if (hasHiddenColumns) {
+    if (hasHiddenColumns)
+    {
         selection = colSel.getVisibleSequenceStrings(start, end, seqs);
-      } else {
+    }
+    else
+    {
         for(i=0; i<iSize; i++)
         {
-          selection[i] = seqs[i].getSequence(start, end);
+          selection[i] = seqs[i].getSequenceAsString(start, end);
         }
 
       }
       return selection;
     }
 
+  public int [][] getVisibleRegionBoundaries(int min, int max)
+  {
+    Vector regions = new Vector();
+    int start = min;
+    int end = max;
+
+    do
+    {
+      if (hasHiddenColumns)
+      {
+        if (start == 0)
+        {
+          start = colSel.adjustForHiddenColumns(start);
+        }
+
+        end = colSel.getHiddenBoundaryRight(start);
+        if (start == end)
+        {
+          end = max;
+        }
+        if (end > max)
+        {
+          end = max;
+        }
+      }
+
+      regions.addElement(new int[]
+                         {start, end});
+
+      if (hasHiddenColumns)
+      {
+        start = colSel.adjustForHiddenColumns(end);
+        start = colSel.getHiddenBoundaryLeft(start) + 1;
+      }
+    }
+    while (end < max);
+
+    int[][] startEnd = new int[regions.size()][2];
+
+    regions.copyInto(startEnd);
+
+    return startEnd;
+
+  }
+
     public boolean getShowHiddenMarkers()
     {
       return showHiddenMarkers;
@@ -1533,7 +1727,9 @@ public class AlignViewport
     public String getSequenceSetId()
     {
       if(sequenceSetID==null)
+    {
         sequenceSetID =  alignment.hashCode()+"";
+    }
 
       return sequenceSetID;
     }
@@ -1541,7 +1737,9 @@ public class AlignViewport
     public void alignmentChanged(AlignmentPanel ap)
     {
         if (padGaps)
+    {
           alignment.padGaps();
+    }
 
         if (hconsensus != null && autoCalculateConsensus)
         {
@@ -1558,16 +1756,20 @@ public class AlignViewport
           {
             SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
             if(sg.getEndRes()>alWidth)
+        {
               sg.setEndRes(alWidth-1);
           }
         }
+    }
 
         if(selectionGroup!=null && selectionGroup.getEndRes()>alWidth)
+    {
           selectionGroup.setEndRes(alWidth-1);
+    }
 
         resetAllColourSchemes();
 
-        alignment.adjustSequenceAnnotations();
+       // alignment.adjustSequenceAnnotations();
     }
 
 
@@ -1605,7 +1807,7 @@ public class AlignViewport
         if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
         {
           ((ClustalxColourScheme)sg.cs).resetClustalX(
-              sg.getSequences(true), sg.getWidth());
+              sg.getSequences(hiddenRepSequences), sg.getWidth());
         }
         sg.recalcConservation();
       }
@@ -1615,21 +1817,51 @@ public class AlignViewport
     public Color getSequenceColour(SequenceI seq)
     {
       if(sequenceColours==null || !sequenceColours.containsKey(seq))
+    {
         return Color.white;
+    }
       else
+    {
         return (Color)sequenceColours.get(seq);
     }
+  }
 
     public void setSequenceColour(SequenceI seq, Color col)
     {
       if(sequenceColours==null)
+    {
         sequenceColours = new Hashtable();
+    }
 
       if(col == null)
+    {
         sequenceColours.remove(seq);
+    }
       else
+    {
         sequenceColours.put(seq, col);
     }
+    }
+    /**
+     * returns the visible column regions of the alignment
+     * @param selectedRegionOnly true to just return the contigs intersecting with the selected area
+     * @return
+     */
+    public int[] getViewAsVisibleContigs(boolean selectedRegionOnly) {
+      int[] viscontigs=null;
+      int start = 0, end = 0;
+      if(selectedRegionOnly && selectionGroup!=null)
+      {
+        start = selectionGroup.getStartRes();
+        end = selectionGroup.getEndRes()+1;
+      }
+      else
+      {
+        end = alignment.getWidth();
+      }
+      viscontigs = colSel.getVisibleContigs(start, end);
+      return viscontigs;
+    }
 
 
 }