X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=997966fa97e8e0fc17bc886afcfced1ff2b4512f;hb=ff2e8d0b23e91c4d7f19dd1922e48e5a718ee0f1;hp=2266462b1a5b04a63ed51775680a04be7d829664;hpb=b7b0de15f5a7c17c0a29008b5e920a1906071d19;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 2266462..997966f 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -1,11 +1,20 @@
 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.*;
+
+import com.sun.image.codec.jpeg.*;
+import java.io.*;
+import java.awt.image.*;
+
+import org.jibble.epsgraphics.*;
+import javax.imageio.*;
+
 
 public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListener, Printable
 {
@@ -14,23 +23,33 @@ 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();
+    IdwidthAdjuster iap = new IdwidthAdjuster(this);
+    idSpaceFillerPanel1.add(iap, BorderLayout.CENTER);
+
+    Dimension d = calculateIdWidth();
+    d.setSize( d.width+4, d.height);
+    idPanel.idCanvas.setPreferredSize( d );
+    hscrollFillerPanel.setPreferredSize( d );
+
     scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
     scorePanelHolder.add(scorePanel, BorderLayout.CENTER);
     seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
@@ -38,37 +57,104 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 
     hscroll.addAdjustmentListener(this);
     vscroll.addAdjustmentListener(this);
-    selectAll(false);
 
     addComponentListener(new ComponentAdapter()
    {
-       public void componentResized(ComponentEvent evt)
+     public void componentResized(ComponentEvent evt)
      {
           RefreshPanels();
      }
    });
 
-  }
 
-  public int countSelected()
-  {
-    return av.getSelection().size();
+  // hscroll.setFocusable(false);
+  // vscroll.setFocusable(false);
+   setFocusable(true);
+
+   addKeyListener(new KeyAdapter()
+   {
+     public void keyPressed(KeyEvent evt)
+     {
+       switch(evt.getKeyCode())
+       {
+         case  27: // escape key
+           av.setSelectionGroup(null);
+           RefreshPanels();
+           break;
+         case KeyEvent.VK_X:
+           alignFrame.cut_actionPerformed(null);
+           break;
+         case KeyEvent.VK_C:
+           alignFrame.copy_actionPerformed(null);
+           break;
+         case KeyEvent.VK_V:
+           alignFrame.paste(true);
+           break;
+         case KeyEvent.VK_A:
+           alignFrame.selectAllSequenceMenuItem_actionPerformed(null);
+           break;
+        case KeyEvent.VK_DOWN:
+          alignFrame.moveSelectedSequences(false);
+          break;
+        case KeyEvent.VK_UP:
+          alignFrame.moveSelectedSequences(true);
+          break;
+        case KeyEvent.VK_F:
+          alignFrame.findMenuItem_actionPerformed(null);
+          break;
+       }
+     }
+   });
   }
 
-  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();
+  Dimension calculateIdWidth()
+  {
+    Graphics g = this.getGraphics();
+    if(g==null)
+    {
+      javax.swing.JFrame f = new javax.swing.JFrame();
+      f.addNotify();
+      g = f.getGraphics();
     }
+
+    FontMetrics fm = g.getFontMetrics(av.font);
+    AlignmentI al = av.getAlignment();
+
+       int i   = 0;
+       int idWidth = 0;
+       String id;
+       while (i < al.getHeight() && al.getSequenceAt(i) != null)
+       {
+         SequenceI s   = al.getSequenceAt(i);
+         if(av.getShowFullId())
+           id   = s.getDisplayId();
+         else
+           id = s.getName();
+
+         if (fm.stringWidth(id) > idWidth)
+           idWidth = fm.stringWidth(id);
+         i++;
+       }
+
+       return new Dimension(idWidth, 12);
   }
 
+
+ 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;
@@ -82,54 +168,134 @@ 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);
 
-      scalePanelHolder.setVisible(!wrap);
-      scorePanelHolder.setVisible(!wrap);
+    hscroll.setVisible(!wrap);
 
-      hscroll.setVisible(!wrap);
-      idSpaceFillerPanel.setVisible(!wrap);
-      idSpaceFillerPanel1.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())
+    {
 
-  public void RefreshPanels()
-  {
-    invalidate();
-    validate();
-    idPanel.idCanvas.paintFlag = true;
-    idPanelHolder.setPreferredSize( idPanel.idCanvas.getPreferredSize() );
-    seqPanel.seqCanvas.paintFlag = true;
-    setScrollValues(av.getStartRes(), av.getStartSeq());
-    av.getConsensus(true);
-    repaint();
+       Alignment al = (Alignment)av.getAlignment();
+       Conservation c = new Conservation("All",
+                            ResidueProperties.propHash, 3, al.getSequences(), 0,
+                            al.getWidth() );
 
-    if(overviewPanel!=null)
-      overviewPanel.updateOverviewImage();
+       c.calculate();
+       c.verdict(false, 100);
+       ConservationColourScheme ccs = new ConservationColourScheme(c, cs);
 
+       av.setGlobalColourScheme( ccs );
+
+    }
+
+    RefreshPanels();
   }
 
+  public void RefreshPanels()
+  {
+              requestFocus();
+              invalidate();
+              idPanelHolder.setPreferredSize(idPanel.idCanvas.getPreferredSize());
+              if(idPanel.idCanvas.getPreferredSize()!=null)
+                hscrollFillerPanel.setPreferredSize(new Dimension(idPanel.idCanvas.getPreferredSize().width, 12));
+              idSpaceFillerPanel1.setPreferredSize(new Dimension(500,
+                  av.charHeight / 2 + 12));
+              scalePanelHolder.setPreferredSize(new Dimension(500,
+                  av.charHeight / 2 + 12));
+              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);
+              if (overviewPanel != null)
+                overviewPanel.updateOverviewImage();
+
+          validate();
+          repaint();
+  }
   int hextent = 0;
   int vextent = 0;
 
+
+  // return value is true if the scroll is valid
+  public boolean scrollUp(boolean up)
+  {
+    if(up)
+    {
+      if(vscroll.getValue()<1)
+        return false;
+      vscroll.setValue(vscroll.getValue() - 1);
+    }
+    else
+    {
+     if(vextent+vscroll.getValue() >= av.getAlignment().getHeight())
+       return false;
+      vscroll.setValue(vscroll.getValue() + 1);
+    }
+
+    return true;
+  }
+
+  public boolean scrollRight(boolean right)
+  {
+    if(right)
+   {
+     if(hscroll.getValue()<1)
+       return false;
+     hscroll.setValue(hscroll.getValue() - 1);
+   }
+   else
+   {
+    if(hextent+hscroll.getValue() >= av.getAlignment().getWidth())
+      return false;
+     hscroll.setValue(hscroll.getValue() + 1);
+   }
+
+   return true;
+ }
+
+
   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 +312,8 @@ 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();
 
   }
@@ -159,43 +326,56 @@ 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());
+      }
+      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();
 
-
     repaint();
   }
 
-
   public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException
   {
-
     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();
+    int pwidth = (int) pf.getImageableWidth();
+    int pheight = (int) pf.getImageableHeight();
+
+    if (av.getWrapAlignment())
+      return printWrappedAlignment(pg, pwidth,pheight, pi);
+    else
+      return printUnwrapped(pg,pwidth, pheight,pi);
+  }
+
+  public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException
+  {
+
+    int idWidth = calculateIdWidth().width;
+
 
-    //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;
@@ -219,17 +399,17 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 
     ////////////////
     //draw Scale
-    pg.translate(idWidth,0);
-    scalePanel.scaleCanvas.drawScale(pg, startRes, endRes, pwidth-idWidth);
+    pg.translate(30,0);
+    scalePanel.drawScale(pg, startRes, endRes, pwidth-idWidth);
 
-    pg.translate(-idWidth, 30);
+    pg.translate(-30, 30);
     ////////////////
     // Draw the ids
     Color currentColor=null;
     Color currentTextColor=null;
     for(int i=startSeq; i<endSeq; i++)
     {
-      if (av.getSelection().contains(av.getAlignment().getSequenceAt(i)))
+      if (av.getSelectionGroup()!=null && av.getSelectionGroup().sequences.contains(av.getAlignment().getSequenceAt(i)))
       {
         currentColor = Color.gray;
         currentTextColor = Color.black;
@@ -242,21 +422,157 @@ 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);
 
-      String string = av.getAlignment().getSequenceAt(i).getDisplayId();
+      String string = av.getAlignment().getSequenceAt(i).getName();
+      if(av.getShowFullId())
+        string = av.getAlignment().getSequenceAt(i).getDisplayId();
+
       pg.drawString(string, 0,  jalview.analysis.AlignmentUtil.getPixelHeight
                     (startSeq, i, av.getCharHeight()) + av.getCharHeight() - (av.getCharHeight() / 5));
     }
 
     // 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);
 
     return Printable.PAGE_EXISTS;
   }
+
+
+  public int printWrappedAlignment(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException
+  {
+
+    int idWidth = calculateIdWidth().width;
+
+    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 = da.getWidth() / chunkWidth;
+
+    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);
+        String string = s.getName();
+        if (av.getShowFullId())
+          string = s.getDisplayId();
+
+        pg.drawString(string, 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.PAGE_EXISTS;
+
+  }
+
+
+  public void makeEPS(int width, int height)
+  {
+    try
+    {
+      jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
+          "LAST_DIRECTORY"), new String[]{"eps"}, "Encapsulated Postscript");
+      chooser.setFileView(new jalview.io.JalviewFileView());
+      chooser.setDialogTitle("Create EPS file from alignment");
+      chooser.setToolTipText("Save");
+
+      int value = chooser.showSaveDialog(this);
+      if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
+        return;
+
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getPath());
+      FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
+      EpsGraphics2D pg = new EpsGraphics2D("Example", out, 0, 0, width, height);
+
+        if (av.getWrapAlignment())
+          printWrappedAlignment(pg, width, height, 0);
+        else
+          printUnwrapped(pg, width, height, 0);
+
+
+        pg.flush();
+        pg.close();
+    }
+    catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
+  }
+
+  public void makePNG(int width, int height)
+  {
+    try
+    {
+      jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
+          "LAST_DIRECTORY"), new String[]{"png"}, "Portable network graphics");
+      chooser.setFileView(new jalview.io.JalviewFileView());
+      chooser.setDialogTitle("Create EPS file from alignment");
+      chooser.setToolTipText("Save");
+
+      int value = chooser.showSaveDialog(this);
+      if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
+        return;
+
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getPath());
+      FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
+
+      BufferedImage bi = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);
+      Graphics png = bi.getGraphics();
+
+
+        if (av.getWrapAlignment())
+          printWrappedAlignment(png, width, height, 0);
+        else
+          printUnwrapped(png, width, height, 0);
+
+        ImageIO.write(bi, "png", out);
+        out.close();
+    }
+    catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
+  }
+
 }
 
+
+
+