X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=775e954551d1bbb6e6ea3c88fd23da18a00f6db5;hb=5f7d80cd8b01e051a6175b0ce8db0ad94d73df2f;hp=53f65d8bdd2e2baf0b664a6dd550d248878d5701;hpb=faa7925a6bfe13bf2ca5f2f2ac3c7afa3027828b;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 53f65d8..775e954 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -1,11 +1,12 @@
 package jalview.gui;
 
 import jalview.jbgui.GAlignmentPanel;
+import jalview.schemes.*;
+import jalview.analysis.*;
+import jalview.datamodel.*;
 import java.awt.*;
-import java.awt.image.*;
 import java.awt.event.*;
 import java.awt.print.*;
-import javax.swing.*;
 
 public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListener, Printable
 {
@@ -14,21 +15,22 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
   OverviewPanel overviewPanel;
   SeqPanel   seqPanel;
   IdPanel    idPanel;
+  SecondaryStructurePanel ssPanel;
   public AlignFrame alignFrame;
   ScalePanel scalePanel;
   ScorePanel scorePanel;
 
-  public boolean    groupEdit = false;
-
-  public AlignmentPanel(AlignFrame af, AlignViewport av)
+  public AlignmentPanel(AlignFrame af, final AlignViewport av)
   {
     alignFrame = af;
     this.av         = av;
     seqPanel        = new SeqPanel  (av, this);
     idPanel         = new IdPanel   (av, this);
-    scalePanel = new ScalePanel(av);
+    scalePanel = new ScalePanel(av, this);
     scorePanel = new ScorePanel(av);
+    ssPanel = new SecondaryStructurePanel(av);
 
+    secondaryPanelHolder.add(ssPanel, BorderLayout.CENTER);
     idPanelHolder.add(idPanel, BorderLayout.CENTER);
     idPanel.addNotify();
     scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
@@ -38,7 +40,6 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 
     hscroll.addAdjustmentListener(this);
     vscroll.addAdjustmentListener(this);
-    selectAll(false);
 
     addComponentListener(new ComponentAdapter()
    {
@@ -48,27 +49,40 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
      }
    });
 
-  }
+   hscroll.setFocusable(false);
+   vscroll.setFocusable(false);
+   setFocusable(true);
+
+   addKeyListener(new KeyAdapter()
+   {
+     public void keyPressed(KeyEvent evt)
+     {
+       if(evt.getKeyCode()==27)
+       {
+         av.setRubberbandGroup(null);
+         RefreshPanels();
+       }
+     }
+   });
 
-  public int countSelected()
-  {
-    return av.getSelection().size();
-  }
 
-  public void selectAll(boolean flag) {
-    int i = 0;
-    if (flag) {
-      while (i < av.getAlignment().getHeight()) {
-        if (! av.getSelection().contains(av.getAlignment().getSequenceAt(i))) {
-          av.getSelection().addElement(av.getAlignment().getSequenceAt(i));
-        }
-        i++;
-      }
-    } else {
-      av.getSelection().clear();
-    }
   }
 
+ public void highlightSearchResults(int [] results)
+ {
+   seqPanel.seqCanvas.highlightSearchResults( results );
+
+   // do we need to scroll the panel?
+   if(results!=null && (av.getStartSeq()>results[0]
+                        || av.getEndSeq()<results[0]
+                        || av.getStartRes()>results[1]
+                        || av.getEndRes()<results[2]))
+       setScrollValues(results[1], results[0]);
+
+
+ }
+
+
  public OverviewPanel getOverviewPanel()
  {
    return overviewPanel;
@@ -82,46 +96,85 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 
   public void setGraphPanelVisible(boolean b)
   {
-    scorePanelHolder.setVisible(b);
     idSpaceFillerPanel.setVisible(b);
+    scorePanelHolder.setVisible(b);
+
+    RefreshPanels();
+    // bit annoying to call this twice, can you do better?
+    RefreshPanels();
+  }
+
+  public void setSecondaryStructureVisible(boolean b)
+  {
+    secondaryPanelHolder.setVisible(b);
     RefreshPanels();
   }
 
   public void setWrapAlignment(boolean wrap)
   {
+    scorePanelHolder.setVisible(!wrap);
+    scalePanelHolder.setVisible(!wrap);
+    secondaryPanelHolder.setVisible(!wrap);
+
+    hscroll.setVisible(!wrap);
 
-      scalePanelHolder.setVisible(!wrap);
-      scorePanelHolder.setVisible(!wrap);
+    idSpaceFillerPanel.setVisible(!wrap);
+    idSpaceFillerPanel1.setVisible(!wrap);
 
-      hscroll.setVisible(!wrap);
-      idSpaceFillerPanel.setVisible(!wrap);
-      idSpaceFillerPanel1.setVisible(!wrap);
+    RefreshPanels();
 
   }
 
 
-  public void setColourScheme(jalview.schemes.ColourSchemeI cs, boolean conservation)
+  public void setColourScheme()
   {
-    seqPanel.setColourScheme(cs, conservation);
-    if(overviewPanel!=null)
-      overviewPanel.updateOverviewImage();
-  }
+    ColourSchemeI cs = av.getGlobalColourScheme();
+
+    if(av.getConservationSelected())
+    {
+
+       Alignment al = (Alignment)av.getAlignment();
+       Conservation c = new Conservation("All",
+                            ResidueProperties.propHash, 3, al.getSequences(), 0,
+                            al.getWidth() );
+
+       c.calculate();
+       c.verdict(false, 100);
+       ConservationColourScheme ccs = new ConservationColourScheme(c, cs);
 
+       av.setGlobalColourScheme( ccs );
+
+    }
+
+    RefreshPanels();
+  }
 
   public void RefreshPanels()
   {
+    requestFocus();
     invalidate();
-    validate();
+    seqPanel.seqCanvas.paintFlag = true;
     idPanel.idCanvas.paintFlag = true;
     idPanelHolder.setPreferredSize( idPanel.idCanvas.getPreferredSize() );
-    seqPanel.seqCanvas.paintFlag = true;
+
+    if(av.getWrapAlignment())
+    {
+      int max = av.alignment.getWidth()/ (seqPanel.seqCanvas.getWidth()/av.charWidth)+1;
+
+      int h  = (av.alignment.getHeight() + 2)*av.charHeight;
+      vextent = seqPanel.seqCanvas.getHeight()/h;
+      vscroll.setValues(0,vextent,0,max);
+    }
+    else
+
     setScrollValues(av.getStartRes(), av.getStartSeq());
     av.getConsensus(true);
-    repaint();
-
     if(overviewPanel!=null)
       overviewPanel.updateOverviewImage();
 
+    validate();
+    repaint();
+
   }
 
   int hextent = 0;
@@ -129,7 +182,7 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 
   public void setScrollValues(int x, int y)
   {
-    hextent = (int)(seqPanel.seqCanvas.getWidth()/av.getCharWidth());
+    hextent = seqPanel.seqCanvas.getWidth()/av.getCharWidth();
     vextent = seqPanel.seqCanvas.getHeight()/av.getCharHeight();
 
     if(hextent+x  >  av.getAlignment().getWidth())
@@ -146,7 +199,8 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 
     hscroll.setValues(x,hextent,0,av.getAlignment().getWidth());
     vscroll.setValues(y,vextent,0,av.getAlignment().getHeight() );
-    seqPanel.seqCanvas.paintFlag = true;
+
+
     repaint();
 
   }
@@ -159,41 +213,62 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     {
       int x = hscroll.getValue();
       av.setStartRes(x);
-      av.setEndRes(x + (int)(seqPanel.seqCanvas.getWidth()/av.getCharWidth()-1));
+      av.setEndRes(x + seqPanel.seqCanvas.getWidth()/av.getCharWidth()-1);
     }
 
     if (evt.getSource() == vscroll)
     {
-        int offy = vscroll.getValue();
+      int offy = vscroll.getValue();
+      if (av.getWrapAlignment())
+      {
+        av.setStartRes( vscroll.getValue() * av.getChunkWidth());
+        // System.out.println(vscroll.getValue()+" "+ av.getChunkWidth());
+      //  int resSpan = av.alignment.getWidth()/ (seqPanel.seqCanvas.getWidth()/av.charWidth)+1;
+     //   int h  = (av.alignment.getHeight() + 2)*av.charHeight;
+      //  vextent = seqPanel.seqCanvas.getHeight()/h;
+     //   vscroll.setValues(0,vextent,0,max);
+
+
+      // av.setStartSeq(  );
+      }
+      else
+      {
         av.setStartSeq(offy);
-        av.setEndSeq(offy + seqPanel.seqCanvas.getHeight()/av.getCharHeight());
+        av.setEndSeq(offy + seqPanel.seqCanvas.getHeight() / av.getCharHeight());
+      }
     }
 
 
     if(overviewPanel!=null)
       overviewPanel.setBoxPosition();
 
-
+    seqPanel.seqCanvas.paintFlag=true;
     repaint();
   }
 
 
-  public int print(Graphics g, PageFormat pf, int pi) throws PrinterException
+
+  public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException
   {
+    if(av.getWrapAlignment())
+    {
+     return PrintWrappedAlignment(pg, pf, pi);
+    }
+
+    pg.translate((int)pf.getImageableX(), (int)pf.getImageableY());
 
     int pwidth = (int)pf.getImageableWidth();
     int pheight = (int)pf.getImageableHeight();
     int idWidth = (int)idPanel.idCanvas.getLabelWidth().getWidth();
 
-    BufferedImage printImage = new BufferedImage(pwidth,pheight,BufferedImage.TYPE_INT_RGB);
-    Graphics pg = printImage.getGraphics();
+
     pg.setColor(Color.white);
     pg.fillRect(0,0,pwidth, pheight);
     pg.setFont( av.getFont() );
 
     ////////////////////////////////////
     /// How many sequences and residues can we fit on a printable page?
-    int totalRes = (int)((pwidth - idWidth)/av.getCharWidth());
+    int totalRes = (pwidth - idWidth)/av.getCharWidth();
     int totalSeq = (int)((pheight - 30)/av.getCharHeight())-1;
     int pagesWide = av.getAlignment().getWidth() / totalRes +1;
     int pagesHigh = av.getAlignment().getHeight() / totalSeq +1;
@@ -240,7 +315,7 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 
       pg.setColor(currentColor);
       pg.fillRect(0,  jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i, av.getCharHeight()),
-                              getWidth(),
+                              idWidth,
                               av.getCharHeight());
 
       pg.setColor(currentTextColor);
@@ -252,36 +327,84 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 
     // draw main sequence panel
     pg.translate(idWidth,0);
+    pg.setClip(0,0,pwidth-idWidth, pheight);
     seqPanel.seqCanvas.drawPanel(pg,startRes,endRes,startSeq,endSeq,startRes,startSeq,0);
 
-
-    g.drawImage( printImage, (int)pf.getImageableX (), (int)pf.getImageableY(), this);
-
-   /* JFrame frame = new JFrame("preview");
-    javax.swing.JPanel p = new preview(printImage);
-    frame.getContentPane().setLayout(new BorderLayout());
-    frame.getContentPane().add(p, java.awt.BorderLayout.CENTER);
-    frame.setVisible(true);
-    frame.setSize(pwidth, pheight);
-
-    frame.validate();*/
-
     return Printable.PAGE_EXISTS;
   }
-}
 
-class preview extends javax.swing.JPanel
-{
-  Image i=null;
-  public preview(Image image)
+  class VPanel extends javax.swing.JPanel
   {
-    i = image;
+    Image image;
+    public VPanel(Image i)
+    {
+      image = i;
+      repaint();
+    }
+    public void paintComponent(Graphics g)
+    {
+      if(image!=null)
+        g.drawImage(image,0,0,this);
+    }
+
   }
 
-  public void paint(Graphics g)
+  public int PrintWrappedAlignment(Graphics pg, PageFormat pf, int pi)
   {
-    if(g!=null)
-      g.drawImage(i, 0,0,null);
+    pg.translate((int)pf.getImageableX(), (int)pf.getImageableY());
+
+    int pwidth = (int)pf.getImageableWidth();
+    int pheight = (int)pf.getImageableHeight();
+    int idWidth = (int)idPanel.idCanvas.getLabelWidth().getWidth();
+
+    if( seqPanel.seqCanvas.getWidth() < pwidth-idWidth)
+      pwidth = seqPanel.seqCanvas.getWidth() + idWidth;
+
+    pg.setColor(Color.white);
+    pg.fillRect(0,0,pwidth, pheight);
+    pg.setFont( av.getFont() );
+
+    ////////////////////////////////////
+    /// How many sequences and residues can we fit on a printable page?
+    AlignmentI da = av.alignment;
+    int endy   = da.getHeight();
+    int chunkHeight =  (da.getHeight() + 2)*av.charHeight;
+    int chunkWidth  =   (pwidth-idWidth)/av.charWidth;
+
+    int noChunksOnPage = pheight / chunkHeight;
+    int totalChunks = endy / chunkHeight;
+
+    if ( pi*noChunksOnPage > totalChunks )
+     return Printable.NO_SUCH_PAGE;
+
+    ////////////////
+    // Draw the ids
+    pg.setClip(0,0,pwidth, noChunksOnPage*chunkHeight);
+
+    int row = pi*noChunksOnPage;
+    pg.setColor(Color.black);
+    for(int ypos=2*av.charHeight;
+        ypos <= pheight && row*chunkWidth<da.getWidth();
+        ypos += chunkHeight, row++ )
+    {
+      for (int i = 0; i < endy; i++)
+      {
+        SequenceI s = da.getSequenceAt(i);
+        pg.drawString(s.getDisplayId(), 0,
+                      AlignmentUtil.getPixelHeight(0, i, av.charHeight) + ypos +
+                      av.charHeight - (av.charHeight / 5));
+      }
+    }
+
+    // draw main sequence panel
+    pg.translate(idWidth,0);
+    seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth-idWidth, pheight, pi*noChunksOnPage*chunkWidth);
+
+
+    return Printable.NO_SUCH_PAGE;//.PAGE_EXISTS;
+
   }
 }
 
+
+