X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=0012ec4765e6141429592ef6541c287c6c5ffcf8;hb=e5f2de91dc41062d8cee8a2a900710f63cf5ae42;hp=a04c5bfcc2802ae8eaec5aa934cfc882f2d0e855;hpb=99f3f01792321efb671ac7ad946efffc3a3319a4;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index a04c5bf..0012ec4 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 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
@@ -27,10 +27,10 @@ import jalview.schemes.*;
 import java.awt.*;
 import java.awt.event.*;
 import java.awt.print.*;
-
 import java.io.*;
-
 import javax.swing.*;
+import java.beans.*;
+
 
 
 /**
@@ -81,146 +81,54 @@ public class AlignmentPanel extends GAlignmentPanel
     annotationPanel = new AnnotationPanel(this);
     alabels = new AnnotationLabels(this);
 
-
     annotationScroller.setViewportView(annotationPanel);
     annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
 
     fontChanged();
 
     scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
-    seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
+   seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
 
     setScrollValues(0, 0);
 
-    annotationPanel.adjustPanelHeight();
-    annotationSpaceFillerHolder.setPreferredSize(annotationPanel.
-                                                 getPreferredSize());
-    annotationScroller.setPreferredSize(annotationPanel.
-                                        getPreferredSize());
     setAnnotationVisible(av.getShowAnnotation());
 
     hscroll.addAdjustmentListener(this);
     vscroll.addAdjustmentListener(this);
 
-    af.addKeyListener(new KeyAdapter()
+    final AlignmentPanel ap = this;
+    av.addPropertyChangeListener(new PropertyChangeListener()
     {
-      public void keyPressed(KeyEvent evt)
+      public void propertyChange(PropertyChangeEvent evt)
       {
-        if(av.cursorMode
-           && evt.getKeyCode()>=KeyEvent.VK_0
-           && evt.getKeyCode()<=KeyEvent.VK_9)
+        if (evt.getPropertyName().equals("alignment"))
         {
-          seqPanel.numberPressed(evt.getKeyChar());
+          PaintRefresher.Refresh(ap,
+                                 av.getSequenceSetId(),
+                                 true,
+                                 true);
+          alignmentChanged();
         }
+      }
+      });
 
-        switch (evt.getKeyCode())
-        {
-          case 27: // escape key
-            av.setSelectionGroup(null);
-            repaint();
-
-            break;
-
-          case KeyEvent.VK_DOWN:
-            if(av.cursorMode)
-            {
-              seqPanel.moveCursor(0,1);
-            }
-            else
-              alignFrame.moveSelectedSequences(false);
-            break;
-
-          case KeyEvent.VK_UP:
-            if (av.cursorMode)
-            {
-              seqPanel.moveCursor(0,-1);
-            }
-            else
-              alignFrame.moveSelectedSequences(true);
-            break;
-
-          case KeyEvent.VK_LEFT:
-            if(av.cursorMode)
-            {
-              seqPanel.moveCursor(-1,0);
-            }
-            break;
+    adjustAnnotationHeight();
 
-          case KeyEvent.VK_RIGHT:
-            if (av.cursorMode)
-            {
-              seqPanel.moveCursor(1,0);
-            }
-            break;
+  }
 
-          case KeyEvent.VK_SPACE:
-            if(av.cursorMode)
-            {
-              seqPanel.insertGapAtCursor(evt.isControlDown());
-            }
-            break;
+  public void alignmentChanged()
+  {
+    av.alignmentChanged(this);
 
-          case KeyEvent.VK_DELETE:
-            if(av.cursorMode)
-            {
-              seqPanel.deleteGapAtCursor(evt.isControlDown());
-              break;
-            }
+    if (overviewPanel != null)
+      overviewPanel.updateOverviewImage();
 
-          case KeyEvent.VK_BACK_SPACE:
-            if(!av.cursorMode)
-            {
-              alignFrame.cut_actionPerformed(null);
-              seqPanel.seqCanvas.repaint();
-            }
-            break;
+    alignFrame.updateEditMenuBar();
 
-          case KeyEvent.VK_Q:
-            if(av.cursorMode)
-            {
-              seqPanel.setSelectionAreaAtCursor(true);
-            }
-            break;
-          case KeyEvent.VK_M:
-            if(av.cursorMode)
-            {
-              seqPanel.setSelectionAreaAtCursor(false);
-            }
-            break;
-
-         case KeyEvent.VK_F2:
-           av.cursorMode = ! av.cursorMode;
-           alignFrame.statusBar.setText("Keyboard editing mode is "+
-               (av.cursorMode ? "on" : "off"));
-           if(av.cursorMode)
-           {
-             seqPanel.seqCanvas.cursorX = av.startRes;
-             seqPanel.seqCanvas.cursorY = av.startSeq;
-           }
-           seqPanel.seqCanvas.repaint();
-           break;
-
-          case KeyEvent.VK_F1:
-            try
-            {
-              ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
-              java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help");
-              javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
+    repaint();
+  }
 
-              javax.help.HelpBroker hb = hs.createHelpBroker();
-              hb.setCurrentID("home");
-              hb.setDisplayed(true);
-            }
-            catch (Exception ex)
-            {
-              ex.printStackTrace();
-            }
-            break;
 
-        }
-      }
-    });
-  }
 
   /**
    * DOCUMENT ME!
@@ -245,19 +153,6 @@ public class AlignmentPanel extends GAlignmentPanel
     idPanel.idCanvas.setPreferredSize(d);
     hscrollFillerPanel.setPreferredSize(d);
 
-    if (av.getWrapAlignment())
-    {
-      int max = av.alignment.getWidth() /
-          seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
-      vscroll.setMaximum(max);
-      vscroll.setUnitIncrement(1);
-      vscroll.setVisibleAmount(1);
-    }
-    else
-    {
-      setScrollValues(av.getStartRes(), av.getStartSeq());
-    }
-
     if (overviewPanel != null)
       overviewPanel.setBoxPosition();
 
@@ -273,7 +168,9 @@ public class AlignmentPanel extends GAlignmentPanel
   {
     Container c = new Container();
 
-    FontMetrics fm = c.getFontMetrics(av.font);
+    FontMetrics fm = c.getFontMetrics(
+      new Font(av.font.getName(), Font.ITALIC, av.font.getSize()));
+
     AlignmentI al = av.getAlignment();
 
     int i = 0;
@@ -344,16 +241,21 @@ public class AlignmentPanel extends GAlignmentPanel
       }
       else
       {
-        int cwidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
-        if( start<av.getStartRes() || start>(av.getStartRes()+cwidth) )
-        {
-          vscroll.setValue(start / cwidth);
-          av.startRes = vscroll.getValue() * cwidth;
-        }
+        scrollToWrappedVisible(start);
       }
     }
   }
 
+  void scrollToWrappedVisible(int res)
+  {
+    int cwidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
+    if( res<=av.getStartRes() || res>=(av.getStartRes()+cwidth) )
+    {
+      vscroll.setValue(res / cwidth);
+      av.startRes = vscroll.getValue() * cwidth;
+    }
+  }
+
   /**
    * DOCUMENT ME!
    *
@@ -389,6 +291,31 @@ public class AlignmentPanel extends GAlignmentPanel
     repaint();
   }
 
+  public void adjustAnnotationHeight()
+  {
+    if (alignFrame.getHeight() == 0)
+    {
+      System.out.println("NEEDS FIXING");
+    }
+
+    int height = annotationPanel.adjustPanelHeight();
+
+    if (height > alignFrame.getHeight() / 2)
+    {
+      height = alignFrame.getHeight() / 2;
+    }
+
+    annotationScroller.setPreferredSize(
+        new Dimension(annotationScroller.getWidth(),
+                      height));
+
+    annotationSpaceFillerHolder.setPreferredSize(new Dimension(
+        annotationSpaceFillerHolder.getWidth(),
+        height));
+
+    repaint();
+  }
+
   /**
    * DOCUMENT ME!
    *
@@ -542,6 +469,7 @@ public class AlignmentPanel extends GAlignmentPanel
    */
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
+
     int oldX = av.getStartRes();
     int oldY = av.getStartSeq();
 
@@ -559,10 +487,26 @@ public class AlignmentPanel extends GAlignmentPanel
 
       if (av.getWrapAlignment())
       {
-        int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.
-            seqCanvas.getWidth());
-        av.setStartRes(vscroll.getValue() * rowSize);
-        av.setEndRes( (vscroll.getValue() + 1) * rowSize);
+        if(offy>-1)
+        {
+          int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.
+              seqCanvas.getWidth());
+          av.setStartRes(offy * rowSize);
+          av.setEndRes( (offy + 1) * rowSize);
+        }
+        else
+        {
+          //This is only called if file loaded is a jar file that
+          //was wrapped when saved and user has wrap alignment true
+          //as preference setting
+          SwingUtilities.invokeLater(new Runnable()
+              {
+                public void run()
+                {
+                  setScrollValues(av.getStartRes(), av.getStartSeq());
+                }
+              });
+        }
       }
       else
       {
@@ -624,13 +568,22 @@ public class AlignmentPanel extends GAlignmentPanel
 
     if (av.getWrapAlignment())
     {
-      int max = av.alignment.getWidth() /
-          seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth()) +1;
+      int maxwidth = av.alignment.getWidth();
 
+      if (av.hasHiddenColumns)
+        maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
 
-      vscroll.setMaximum(max);
-      vscroll.setUnitIncrement(1);
-      vscroll.setVisibleAmount(1);
+      int canvasWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
+            if(canvasWidth>0)
+      {
+        int max = maxwidth /
+            seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.
+            getWidth()) +
+            1;
+        vscroll.setMaximum(max);
+        vscroll.setUnitIncrement(1);
+        vscroll.setVisibleAmount(1);
+      }
     }
     else
     {
@@ -640,7 +593,6 @@ public class AlignmentPanel extends GAlignmentPanel
     if( this.getVisibleRect().getBounds() == g.getClipBounds()
         && overviewPanel != null)
         overviewPanel.updateOverviewImage();
-
   }
 
   /**
@@ -687,7 +639,7 @@ public class AlignmentPanel extends GAlignmentPanel
   public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi)
       throws PrinterException
   {
-    int idWidth = calculateIdWidth().width + 4;
+    int idWidth = getVisibleIdWidth();
     FontMetrics fm = getFontMetrics(av.getFont());
     int scaleHeight = av.charHeight + fm.getDescent();
 
@@ -762,18 +714,19 @@ public class AlignmentPanel extends GAlignmentPanel
     pg.setFont(new Font(av.getFont().getName(),
                         Font.ITALIC,
                         av.getFont().getSize()));
+    SequenceI seq;
     for (int i = startSeq; i < endSeq; i++)
     {
+      seq = av.getAlignment().getSequenceAt(i);
       if ( (av.getSelectionGroup() != null) &&
-          av.getSelectionGroup().sequences.contains(
-              av.getAlignment().getSequenceAt(i)))
+          av.getSelectionGroup().getSequences(false).contains(seq))
       {
         currentColor = Color.gray;
         currentTextColor = Color.black;
       }
       else
       {
-        currentColor = av.getAlignment().getSequenceAt(i).getColor();
+        currentColor = av.getSequenceColour(seq);
         currentTextColor = Color.black;
       }
 
@@ -783,10 +736,8 @@ public class AlignmentPanel extends GAlignmentPanel
 
       pg.setColor(currentTextColor);
 
-      String string = av.getAlignment().getSequenceAt(i).getDisplayId
-          ( av.getShowJVSuffix());
-
-      pg.drawString(string, 0,
+      pg.drawString(seq.getDisplayId( av.getShowJVSuffix()),
+                    0,
                     ( ( (i - startSeq) * av.charHeight) + av.getCharHeight()) -
                     (av.getCharHeight() / 5));
     }
@@ -842,12 +793,17 @@ public class AlignmentPanel extends GAlignmentPanel
         + hgap
         + annotationHeight;
 
-    int idWidth = calculateIdWidth().width + 4;
+    int idWidth = getVisibleIdWidth();
+
+    int maxwidth = av.alignment.getWidth();
+    if (av.hasHiddenColumns)
+      maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+
 
     int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth -
         idWidth);
 
-    int totalHeight = cHeight * (av.alignment.getWidth() / resWidth + 1);
+    int totalHeight = cHeight * (maxwidth / resWidth + 1);
 
     pg.setColor(Color.white);
     pg.fillRect(0, 0, pwidth, pheight);
@@ -910,26 +866,42 @@ public class AlignmentPanel extends GAlignmentPanel
     }
   }
 
+  int getVisibleIdWidth()
+  {
+    return
+        idPanel.getWidth() > 0 ? idPanel.getWidth() :
+        calculateIdWidth().width + 4;
+  }
+
   void makeAlignmentImage(int type, File file)
   {
-    int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;
-    int width = idPanel.getWidth() + (av.alignment.getWidth() * av.charWidth);
+    int maxwidth = av.alignment.getWidth();
+    if (av.hasHiddenColumns)
+      maxwidth = av.getColumnSelection().findColumnPosition(maxwidth);
 
-    if (idPanel.getWidth() == 0)
-    {
-      width += calculateIdWidth().getWidth() + 4;
-    }
+    int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;
+    int width = getVisibleIdWidth() + (maxwidth * av.charWidth);
 
     if (av.getWrapAlignment())
     {
       height = getWrappedHeight();
-      width = seqPanel.getWidth() + idPanel.getWidth();
+      if (System.getProperty("java.awt.headless") != null
+          && System.getProperty("java.awt.headless").equals("true"))
+      {
+        width = alignFrame.getWidth() - 22;
+      }
+      else
+        width = seqPanel.getWidth() + getVisibleIdWidth();
+
     }
     else if (av.getShowAnnotation())
     {
       height += annotationPanel.adjustPanelHeight() + 3;
     }
 
+    try
+    {
+
     jalview.util.ImageMaker im;
     if(type==jalview.util.ImageMaker.PNG)
       im  = new jalview.util.ImageMaker(this,
@@ -942,8 +914,6 @@ public class AlignmentPanel extends GAlignmentPanel
                                        "Create EPS file from alignment",
                                         width, height, file, alignFrame.getTitle() );
 
-    try
-    {
       if (av.getWrapAlignment())
       {
         if(im.getGraphics()!=null)
@@ -1002,7 +972,7 @@ public class AlignmentPanel extends GAlignmentPanel
   {
     ///////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS
     //////////////////////////////////////////////
-    int idWidth = calculateIdWidth().width + 4;
+    int idWidth = getVisibleIdWidth();
     FontMetrics fm = getFontMetrics(av.getFont());
     int scaleHeight = av.charHeight + fm.getDescent();
 
@@ -1096,9 +1066,9 @@ public class AlignmentPanel extends GAlignmentPanel
                       if (features[f].getDescription() != null && !features[f].getType().equals(features[f].getDescription()))
                         text.append(" " + features[f].getDescription());
 
-                      if (features[f].getStatus() != null && features[f].getStatus().length()>0)
+                      if (features[f].getValue("status") != null )
                       {
-                        text.append(" (" + features[f].getStatus() + ")");
+                        text.append(" (" + features[f].getValue("status") + ")");
                       }
                     }
                   }
@@ -1126,9 +1096,18 @@ public class AlignmentPanel extends GAlignmentPanel
 
   int getWrappedHeight()
   {
+    int seqPanelWidth = seqPanel.seqCanvas.getWidth();
+
+    //If headless, seqPanel will have 0 width
+    if (System.getProperty("java.awt.headless") != null
+              && System.getProperty("java.awt.headless").equals("true"))
+    {
+      seqPanelWidth = alignFrame.getWidth() - getVisibleIdWidth();
+    }
 
     int chunkWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(
-        seqPanel.seqCanvas.getWidth());
+        seqPanelWidth
+          );
 
     int hgap = av.charHeight;
     if (av.scaleAboveWrapped)
@@ -1144,7 +1123,12 @@ public class AlignmentPanel extends GAlignmentPanel
         + hgap
         + annotationHeight;
 
-    int height = ( (av.alignment.getWidth() / chunkWidth) + 1) * cHeight;
+    int maxwidth = av.alignment.getWidth();
+    if (av.hasHiddenColumns)
+      maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+
+
+    int height = ( (maxwidth / chunkWidth) + 1) * cHeight;
 
     return height;
   }