X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=f6e6114c4a7f7762584684d49ff1621603026188;hb=5fa8d710ac4197020961cb28556081ed294359dc;hp=12c1cbd383bbbe7fbdfbbd32e94ed9857826a58a;hpb=95a46891288f4fc63d690cab4f56879678f54fb6;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 12c1cbd..f6e6114 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -18,8 +18,6 @@
  */
 package jalview.gui;
 
-import jalview.analysis.*;
-
 import jalview.datamodel.*;
 
 import jalview.jbgui.*;
@@ -151,12 +149,30 @@ public class AlignmentPanel extends GAlignmentPanel
                 av.charHeight + fm.getDescent()));
 
         idPanel.idCanvas.gg = null;
+        seqPanel.seqCanvas.img = null;
         annotationPanel.adjustPanelHeight();
 
         Dimension d = calculateIdWidth();
         d.setSize(d.width + 4, d.height);
         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();
+
         repaint();
     }
 
@@ -283,14 +299,23 @@ public class AlignmentPanel extends GAlignmentPanel
      */
     public void setWrapAlignment(boolean wrap)
     {
+        av.startSeq = 0;
         scalePanelHolder.setVisible(!wrap);
         hscroll.setVisible(!wrap);
         idwidthAdjuster.setVisible(!wrap);
 
-        av.setShowAnnotation(!wrap);
-        annotationScroller.setVisible(!wrap);
-        annotationSpaceFillerHolder.setVisible(!wrap);
-        idSpaceFillerPanel1.setVisible(!wrap);
+       if(wrap)
+       {
+         annotationScroller.setVisible(false);
+         annotationSpaceFillerHolder.setVisible(false);
+       }
+       else if(av.showAnnotation)
+       {
+         annotationScroller.setVisible(true);
+         annotationSpaceFillerHolder.setVisible(true);
+       }
+
+       idSpaceFillerPanel1.setVisible(!wrap);
 
         repaint();
     }
@@ -408,14 +433,6 @@ public class AlignmentPanel extends GAlignmentPanel
         vscroll.setValues(y, vextent, 0, av.getAlignment().getHeight());
     }
 
-    public void this_mouseWheelMoved(MouseWheelEvent e)
-    {
-      if(e.getWheelRotation()>0)
-        scrollUp(false);
-      else
-        scrollUp(true);
-    }
-
 
     /**
      * DOCUMENT ME!
@@ -424,6 +441,7 @@ public class AlignmentPanel extends GAlignmentPanel
      */
     public void adjustmentValueChanged(AdjustmentEvent evt)
     {
+
         int oldX = av.getStartRes();
         int oldY = av.getStartSeq();
 
@@ -458,21 +476,28 @@ public class AlignmentPanel extends GAlignmentPanel
             overviewPanel.setBoxPosition();
         }
 
-        if (av.getWrapAlignment() || !fastPaint)
+        int xShift = av.getStartRes() - oldX;
+        int yShift = av.getStartSeq() - oldY;
+
+        if ( (xShift != 0 && yShift != 0) ||
+            (Math.abs(xShift) > av.getEndRes() - av.getStartRes()
+             || Math.abs(yShift) > av.getEndSeq() - av.getStartSeq())
+             || av.getWrapAlignment()
+             || !fastPaint)
         {
-            repaint();
+          // Either no shift at all, or shift greater than visible amount
+          repaint();
         }
         else
         {
-            idPanel.idCanvas.fastPaint(av.getStartSeq() - oldY);
-            seqPanel.seqCanvas.fastPaint(av.getStartRes() - oldX,
-                av.getStartSeq() - oldY);
+            idPanel.idCanvas.fastPaint(yShift);
+            seqPanel.seqCanvas.fastPaint(xShift, yShift);
 
             scalePanel.repaint();
 
             if (av.getShowAnnotation())
             {
-                annotationPanel.fastPaint(av.getStartRes() - oldX);
+                annotationPanel.fastPaint(xShift);
             }
         }
     }
@@ -746,6 +771,33 @@ public class AlignmentPanel extends GAlignmentPanel
      */
     public void makeEPS(File epsFile)
     {
+      boolean accurateText = true;
+
+      String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
+          "Prompt each time");
+
+      // If we need to prompt, and if the GUI is visible then
+      // Prompt for EPS rendering style
+      if (renderStyle.equalsIgnoreCase("Prompt each time")
+          && !
+          (System.getProperty("java.awt.headless") != null
+           && System.getProperty("java.awt.headless").equals("true")))
+      {
+        EPSOptions eps = new EPSOptions();
+        renderStyle = eps.getValue();
+
+        if(eps.cancelled || renderStyle==null)
+          return;
+
+        renderStyle = eps.getValue();
+      }
+
+      if (renderStyle.equalsIgnoreCase("text"))
+      {
+        accurateText = false;
+      }
+
+
         if(epsFile == null)
         {
           jalview.io.JalviewFileChooser chooser = new jalview.io.
@@ -791,12 +843,14 @@ public class AlignmentPanel extends GAlignmentPanel
 
         try
          {
-            FileOutputStream out = new FileOutputStream(epsFile);
-            EpsGraphics2D pg = new EpsGraphics2D("Example", out, 0, 0, width,
-                    height);
+           FileOutputStream out = new FileOutputStream(epsFile);
+           EpsGraphics2D pg = new EpsGraphics2D("Example", out, 0, 0, width,
+                                                height);
 
-            if (av.getWrapAlignment())
-            {
+           pg.setAccurateTextMode(accurateText);
+
+           if (av.getWrapAlignment())
+           {
                 printWrappedAlignment(pg, width, height, 0);
             }
             else
@@ -806,7 +860,22 @@ public class AlignmentPanel extends GAlignmentPanel
 
             pg.flush();
             pg.close();
-        }
+          }
+          catch (OutOfMemoryError err)
+          {
+            System.out.println("########################\n"
+                               + "OUT OF MEMORY " + epsFile + "\n"
+                               + "########################");
+
+            JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                                                  "Out of memory creating EPS file!!"
+                                                  +
+                                                  "\nSee help files for increasing Java Virtual Machine memory."
+                                                  , "Out of memory",
+                                                  JOptionPane.WARNING_MESSAGE);
+            System.out.println("Create EPS: " + err);
+            System.gc();
+          }
         catch (Exception ex)
         {
             ex.printStackTrace();
@@ -953,11 +1022,21 @@ public class AlignmentPanel extends GAlignmentPanel
             ImageIO.write(bi, "png", out);
             out.close();
         }
-        catch(OutOfMemoryError err)
+        catch (OutOfMemoryError err)
         {
           System.out.println("########################\n"
-                             +"OUT OF MEMORY "+pngFile+"\n"
-                             +"########################");
+                             + "OUT OF MEMORY " + pngFile + "\n"
+                             + "########################");
+
+          JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                                                "Out of memory creating PNG!!"
+                                                +
+                                                "\nSee help files for increasing Java Virtual Machine memory."
+                                                , "Out of memory",
+                                                JOptionPane.WARNING_MESSAGE);
+          System.out.println("Create PNG: " + err);
+          System.gc();
+
         }
         catch (Exception ex)
         {