X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=fde4d90e18bbf9f5c2b1e09f3aac7850c817c9a6;hb=2ef43e1e505af2742f1c3a59619c8a4357ea82c4;hp=23d7612882a0e987cde599a647f6b45cbf2e237b;hpb=0125a426aecc7065538a13f48236dc1e8d268044;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 23d7612..fde4d90 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -61,8 +61,9 @@ public class AlignViewport
     SequenceGroup selectionGroup;
     int charHeight;
     int charWidth;
+    boolean validCharWidth;
     int wrappedWidth;
-    Font font = new Font("SansSerif", Font.PLAIN, 10);
+    Font font;
     AlignmentI alignment;
     ColumnSelection colSel = new ColumnSelection();
     int threshold;
@@ -73,6 +74,9 @@ public class AlignViewport
     boolean scaleRightWrapped = true;
     boolean hasHiddenColumns = false;
     boolean hasHiddenRows = false;
+    boolean showHiddenMarkers = true;
+
+    boolean cursorMode = false;
 
     // The following vector holds the features which are
     // currently visible, in the correct order or rendering
@@ -84,6 +88,7 @@ public class AlignViewport
     AlignmentAnnotation consensus;
     AlignmentAnnotation conservation;
     AlignmentAnnotation quality;
+    boolean autoCalculateConsensus = true;
 
     /** DOCUMENT ME!! */
     public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
@@ -97,6 +102,8 @@ public class AlignViewport
 
     boolean antiAlias = false;
 
+    boolean padGaps = false;
+
 
     public AlignViewport(AlignmentI al, boolean dataset)
     {
@@ -114,6 +121,20 @@ public class AlignViewport
         setAlignment(al);
         init();
     }
+    /**
+     * Create a new AlignViewport with hidden regions
+     * @param al AlignmentI
+     * @param hiddenColumns ColumnSelection
+     */
+    public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns) {
+      setAlignment(al);
+      if (hiddenColumns!=null) {
+        this.colSel = hiddenColumns;
+        if (hiddenColumns.getHiddenColumns() != null)
+          hasHiddenColumns = true;
+      }
+      init();
+    }
 
     void init()
     {
@@ -131,6 +152,10 @@ public class AlignViewport
       showQuality = Cache.getDefault("SHOW_QUALITY", true);
       showIdentity = Cache.getDefault("SHOW_IDENTITY", true);
 
+      autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
+
+      padGaps = Cache.getDefault("PAD_GAPS", false);
+
        String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
        String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "") ;
        String fontSize = Cache.getDefault("FONT_SIZE", "10");
@@ -308,12 +333,19 @@ public class AlignViewport
       }
       catch (OutOfMemoryError error)
       {
-        javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
-            "Out of memory calculating conservation!!"
-            +
-            "\nSee help files for increasing Java Virtual Machine memory."
-            , "Out of memory",
-            javax.swing.JOptionPane.WARNING_MESSAGE);
+        javax.swing.SwingUtilities.invokeLater(new Runnable()
+        {
+          public void run()
+          {
+            javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                "Out of memory calculating conservation!!"
+                +
+                "\nSee help files for increasing Java Virtual Machine memory."
+                , "Out of memory",
+                javax.swing.JOptionPane.WARNING_MESSAGE);
+          }
+        });
+
         System.out.println("Conservation calculation: " + error);
         System.gc();
 
@@ -393,12 +425,20 @@ public class AlignViewport
 
       }catch(OutOfMemoryError error)
       {
-        javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
-            "Out of memory calculating consensus!!"
-            +
-            "\nSee help files for increasing Java Virtual Machine memory."
-            , "Out of memory",
-            javax.swing.JOptionPane.WARNING_MESSAGE);
+        javax.swing.SwingUtilities.invokeLater(new Runnable()
+        {
+          public void run()
+          {
+            javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                "Out of memory calc45ulating consensus!!"
+                +
+                "\nSee help files for increasing Java Virtual Machine memory."
+                , "Out of memory",
+                javax.swing.JOptionPane.WARNING_MESSAGE);
+          }
+        });
+
+
         System.out.println("Consensus calculation: " + error);
         System.gc();
       }
@@ -600,6 +640,7 @@ public class AlignViewport
         java.awt.FontMetrics fm = c.getFontMetrics(font);
         setCharHeight(fm.getHeight());
         setCharWidth(fm.charWidth('M'));
+        validCharWidth = true;
     }
 
     /**
@@ -846,41 +887,6 @@ public class AlignViewport
         return increment;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param y DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getIndex(int y)
-    {
-        int y1 = 0;
-        int starty = getStartSeq();
-        int endy = getEndSeq();
-
-        for (int i = starty; i <= endy; i++)
-        {
-            if ((i < alignment.getHeight()) &&
-                    (alignment.getSequenceAt(i) != null))
-            {
-                int y2 = y1 + getCharHeight();
-
-                if ((y >= y1) && (y <= y2))
-                {
-                    return i;
-                }
-
-                y1 = y2;
-            }
-            else
-            {
-                return -1;
-            }
-        }
-
-        return -1;
-    }
 
     /**
      * DOCUMENT ME!
@@ -1093,10 +1099,36 @@ public class AlignViewport
       return isDataset;
     }
 
+
+    public void hideSelectedColumns()
+    {
+      if (colSel.size() < 1)
+        return;
+
+      colSel.hideSelectedColumns();
+      setSelectionGroup(null);
+
+      hasHiddenColumns = true;
+    }
+
+
+    public void hideColumns(int start, int end)
+    {
+      if(start==end)
+        colSel.hideColumns(start);
+      else
+        colSel.hideColumns(start, end);
+      setSelectionGroup(null);
+      hasHiddenColumns = true;
+    }
+
     public void hideSequence(SequenceI seq)
     {
-      alignment.getHiddenSequences().hideSequence(seq);
-      hasHiddenRows = true;
+      if(seq!=null)
+      {
+        alignment.getHiddenSequences().hideSequence(seq);
+        hasHiddenRows = true;
+      }
     }
 
     public void showSequence(int index)
@@ -1107,8 +1139,232 @@ public class AlignViewport
         hasHiddenRows = false;
     }
 
+    public void showColumn(int col)
+    {
+      colSel.revealHiddenColumns(col);
+      if(colSel.getHiddenColumns()==null)
+        hasHiddenColumns = false;
+    }
+
+    public void showAllHiddenColumns()
+    {
+      colSel.revealAllHiddenColumns();
+      hasHiddenColumns = false;
+    }
+
+    public void showAllHiddenSeqs()
+    {
+      if(alignment.getHiddenSequences().getSize()>0)
+      {
+        alignment.getHiddenSequences().showAll();
+        hasHiddenRows = false;
+      }
+    }
+
     public int adjustForHiddenSeqs(int alignmentIndex)
     {
       return alignment.getHiddenSequences().adjustForHiddenSeqs(alignmentIndex);
     }
+
+    /**
+     * This method returns the a new SequenceI [] with
+     * the selection sequence and start and end points adjusted
+     * @return String[]
+     */
+    public SequenceI[] getSelectionAsNewSequence()
+    {
+      SequenceI[] sequences;
+
+      if (selectionGroup == null)
+        sequences = alignment.getSequencesArray();
+      else
+        sequences = selectionGroup.getSelectionAsNewSequences(alignment);
+
+      return sequences;
+    }
+
+    /**
+     * This method returns the visible alignment as text, as
+     * seen on the GUI, ie if columns are hidden they will not
+     * be returned in the result.
+     * Use this for calculating trees, PCA, redundancy etc on views
+     * which contain hidden columns.
+     * @return String[]
+     */
+    public jalview.datamodel.CigarArray getViewAsCigars(boolean selectedRegionOnly)
+    {
+      CigarArray selection=null;
+      SequenceI [] seqs= null;
+      int i, iSize;
+      int start = 0, end = 0;
+      if(selectedRegionOnly && selectionGroup!=null)
+      {
+        iSize = selectionGroup.getSize(false);
+        seqs = selectionGroup.getSequencesInOrder(alignment);
+        start = selectionGroup.getStartRes();
+        end = selectionGroup.getEndRes(); // inclusive for start and end in SeqCigar constructor
+      }
+      else
+      {
+        iSize = alignment.getHeight();
+        seqs = alignment.getSequencesArray();
+        end = alignment.getWidth()-1;
+      }
+      SeqCigar[] selseqs = new SeqCigar[iSize];
+      for(i=0; i<iSize; i++)
+      {
+        selseqs[i] = new SeqCigar(seqs[i], start, end);
+      }
+      selection=new CigarArray(selseqs);
+      // now construct the CigarArray operations
+      if (hasHiddenColumns) {
+        Vector regions = colSel.getHiddenColumns();
+        int [] region;
+        int hideStart, hideEnd;
+        int last=start;
+        for (int j = 0; last<end & j < regions.size(); j++)
+        {
+          region = (int[]) regions.elementAt(j);
+          hideStart = region[0];
+          hideEnd = region[1];
+          // edit hidden regions to selection range
+          if(hideStart<last) {
+            if (hideEnd > last)
+            {
+              hideStart = last;
+            } 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);
+      } else {
+        selection.addOperation(CigarArray.M, end-start);
+      }
+      return selection;
+    }
+    /**
+     * return a compact representation of the current alignment selection to
+     * pass to an analysis function
+     * @param selectedOnly boolean true to just return the selected view
+     * @return AlignmentView
+     */
+    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)
+        return new AlignmentView(aligview);
+      return null;
+    }
+    /**
+     * This method returns the visible alignment as text, as
+     * seen on the GUI, ie if columns are hidden they will not
+     * be returned in the result.
+     * Use this for calculating trees, PCA, redundancy etc on views
+     * which contain hidden columns.
+     * @return String[]
+     */
+    public String [] getViewAsString(boolean selectedRegionOnly)
+    {
+      String [] selection = null;
+      SequenceI [] seqs= null;
+      int i, iSize;
+      int start = 0, end = 0;
+      if(selectedRegionOnly && selectionGroup!=null)
+      {
+        iSize = selectionGroup.getSize(false);
+        seqs = selectionGroup.getSequencesInOrder(alignment);
+        start = selectionGroup.getStartRes();
+        end = selectionGroup.getEndRes()+1;
+      }
+      else
+      {
+        iSize = alignment.getHeight();
+        seqs = alignment.getSequencesArray();
+        end = alignment.getWidth();
+      }
+
+      selection = new String[iSize];
+
+
+      for(i=0; i<iSize; i++)
+      {
+        if (hasHiddenColumns)
+        {
+             StringBuffer visibleSeq = new StringBuffer();
+             Vector regions = colSel.getHiddenColumns();
+
+             int blockStart = start, blockEnd=end;
+             int [] region;
+             int hideStart, hideEnd;
+
+             for (int j = 0; j < regions.size(); j++)
+             {
+               region = (int[]) regions.elementAt(j);
+               hideStart = region[0];
+               hideEnd = region[1];
+
+               if(hideStart < start)
+               {
+                 continue;
+               }
+
+               blockStart = Math.min(blockStart, hideEnd+1);
+               blockEnd = Math.min(blockEnd, hideStart);
+
+               if(blockStart>blockEnd)
+               {
+                  break;
+               }
+
+
+               visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd));
+
+               blockStart = hideEnd+1;
+               blockEnd = end;
+             }
+
+             if(end>blockStart)
+               visibleSeq.append(seqs[i].getSequence(blockStart, end));
+
+             selection[i] = visibleSeq.toString();
+        }
+        else
+        {
+          selection[i] = seqs[i].getSequence(start, end);
+        }
+      }
+
+      return selection;
+    }
+
+    public boolean getShowHiddenMarkers()
+    {
+      return showHiddenMarkers;
+    }
+
+    public void setShowHiddenMarkers(boolean show)
+    {
+      showHiddenMarkers = show;
+    }
 }