Wrap alignment with annotations

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 6627941..3420993 100755 (executable)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -61,8 +61,7 @@ public class AlignViewport
     SequenceGroup selectionGroup;\r
     int charHeight;\r
     int charWidth;\r
-    int chunkWidth;\r
-    int chunkHeight;\r
+    int wrappedWidth;\r
     Font font = new Font("SansSerif", Font.PLAIN, 10);\r
     AlignmentI alignment;\r
     ColumnSelection colSel = new ColumnSelection();\r
@@ -630,9 +629,9 @@ public class AlignViewport
      *\r
      * @param w DOCUMENT ME!\r
      */\r
-    public void setChunkWidth(int w)\r
+    public void setWrappedWidth(int w)\r
     {\r
-        this.chunkWidth = w;\r
+        this.wrappedWidth = w;\r
     }\r
 \r
     /**\r
@@ -640,30 +639,11 @@ public class AlignViewport
      *\r
      * @return DOCUMENT ME!\r
      */\r
-    public int getChunkWidth()\r
+    public int getWrappedWidth()\r
     {\r
-        return chunkWidth;\r
+        return wrappedWidth;\r
     }\r
 \r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param h DOCUMENT ME!\r
-     */\r
-    public void setChunkHeight(int h)\r
-    {\r
-        this.chunkHeight = h;\r
-    }\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @return DOCUMENT ME!\r
-     */\r
-    public int getChunkHeight()\r
-    {\r
-        return chunkHeight;\r
-    }\r
 \r
     /**\r
      * DOCUMENT ME!\r

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index f6e6114..8f5c74c 100755 (executable)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -47,7 +47,7 @@ import javax.swing.*;
 public class AlignmentPanel extends GAlignmentPanel\r
     implements AdjustmentListener, Printable\r
 {\r
-    AlignViewport av;\r
+    public AlignViewport av;\r
     OverviewPanel overviewPanel;\r
     SeqPanel seqPanel;\r
     IdPanel idPanel;\r
@@ -134,6 +134,7 @@ public class AlignmentPanel extends GAlignmentPanel
             });\r
     }\r
 \r
+\r
     /**\r
      * DOCUMENT ME!\r
      */\r
@@ -625,7 +626,7 @@ public class AlignmentPanel extends GAlignmentPanel
 \r
         if (av.showAnnotation)\r
         {\r
-            pagesHigh += annotationPanel.getHeight();\r
+            pagesHigh += annotationPanel.adjustPanelHeight()+3;\r
         }\r
 \r
         pagesHigh /= pheight;\r
@@ -685,7 +686,7 @@ public class AlignmentPanel extends GAlignmentPanel
 \r
         if (av.showAnnotation && (endSeq == av.alignment.getHeight()))\r
         {\r
-            pg.translate(-idWidth, (endSeq - startSeq) * av.charHeight);\r
+            pg.translate(-idWidth, (endSeq - startSeq) * av.charHeight +3);\r
             alabels.drawComponent((Graphics2D) pg);\r
             pg.translate(idWidth, 0);\r
             annotationPanel.drawComponent((Graphics2D) pg, startRes, endRes +\r
@@ -710,17 +711,32 @@ public class AlignmentPanel extends GAlignmentPanel
     public int printWrappedAlignment(Graphics pg, int pwidth, int pheight,\r
         int pi) throws PrinterException\r
     {\r
-        int idWidth = calculateIdWidth().width + 4;\r
+\r
+      int annotationHeight = 0;\r
+      if (av.showAnnotation)\r
+        annotationHeight = annotationPanel.adjustPanelHeight();\r
+\r
+      int hgap = av.charHeight;\r
+      if (av.scaleAboveWrapped)\r
+        hgap += av.charHeight;\r
+\r
+      int cHeight = av.getAlignment().getHeight() * av.charHeight\r
+          + hgap\r
+          + annotationHeight;\r
+\r
+\r
+      int idWidth = calculateIdWidth().width + 4;\r
 \r
         int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth -\r
                 idWidth);\r
-        int totalHeight = totalHeight = (av.alignment.getHeight() + 2) * ((av.alignment.getWidth() / resWidth) +\r
-                1) * av.charHeight;\r
+\r
+        int totalHeight = cHeight * (av.alignment.getWidth() / resWidth +1);\r
 \r
         pg.setColor(Color.white);\r
         pg.fillRect(0, 0, pwidth, pheight);\r
         pg.setFont(av.getFont());\r
 \r
+\r
         ////////////////\r
         // Draw the ids\r
         pg.setColor(Color.black);\r
@@ -729,7 +745,7 @@ public class AlignmentPanel extends GAlignmentPanel
 \r
         pg.setClip(0, pi * pheight, pwidth, pheight);\r
 \r
-        int ypos = 2 * av.charHeight;\r
+        int ypos = hgap;\r
 \r
         do\r
         {\r
@@ -748,7 +764,7 @@ public class AlignmentPanel extends GAlignmentPanel
                     (av.charHeight / 5));\r
             }\r
 \r
-            ypos += ((av.alignment.getHeight() + 2) * av.charHeight);\r
+            ypos += cHeight;\r
         }\r
         while (ypos < totalHeight);\r
 \r
@@ -759,8 +775,9 @@ public class AlignmentPanel extends GAlignmentPanel
         if ((pi * pheight) < totalHeight)\r
         {\r
             return Printable.PAGE_EXISTS;\r
+\r
         }\r
-        else\r
+     else\r
         {\r
             return Printable.NO_SUCH_PAGE;\r
         }\r
@@ -824,23 +841,22 @@ public class AlignmentPanel extends GAlignmentPanel
                                         chooser.getSelectedFile().getParent());\r
         }\r
 \r
+\r
         int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;\r
         int width = idPanel.getWidth() + (av.alignment.getWidth() * av.charWidth);\r
 \r
+\r
         if (av.getWrapAlignment())\r
         {\r
-          height = ( (av.alignment.getWidth() / av.getChunkWidth()) + 1) *\r
-              av.chunkHeight;\r
+          height = getWrappedHeight();\r
           width = seqPanel.getWidth() + idPanel.getWidth();\r
-\r
         }\r
-\r
-\r
-        if (av.getShowAnnotation())\r
+        else if (av.getShowAnnotation())\r
         {\r
-            height += annotationPanel.getPreferredSize().height;\r
+          height += annotationPanel.adjustPanelHeight()+3;\r
         }\r
 \r
+\r
         try\r
          {\r
            FileOutputStream out = new FileOutputStream(epsFile);\r
@@ -948,6 +964,32 @@ public class AlignmentPanel extends GAlignmentPanel
 \r
     }\r
 \r
+    int getWrappedHeight()\r
+    {\r
+\r
+      int chunkWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(\r
+        seqPanel.seqCanvas.getWidth());\r
+\r
+      int hgap = av.charHeight;\r
+      if (av.scaleAboveWrapped)\r
+        hgap += av.charHeight;\r
+\r
+      int annotationHeight = 0;\r
+      if (av.showAnnotation)\r
+      {\r
+        annotationHeight = annotationPanel.adjustPanelHeight();\r
+      }\r
+\r
+      int cHeight = av.getAlignment().getHeight() * av.charHeight\r
+          + hgap\r
+          + annotationHeight;\r
+\r
+\r
+      int height =  ( (av.alignment.getWidth() / chunkWidth) + 1) * cHeight;\r
+\r
+      return height;\r
+    }\r
+\r
     /**\r
      * DOCUMENT ME!\r
      */\r
@@ -986,16 +1028,12 @@ public class AlignmentPanel extends GAlignmentPanel
 \r
       if (av.getWrapAlignment())\r
       {\r
-        height = ( (av.alignment.getWidth() / av.getChunkWidth()) + 1) *\r
-            av.chunkHeight;\r
+        height = getWrappedHeight();\r
         width = seqPanel.getWidth() + idPanel.getWidth();\r
-\r
       }\r
-\r
-\r
-        if (av.getShowAnnotation())\r
+      else if (av.getShowAnnotation())\r
         {\r
-            height += annotationPanel.getPreferredSize().height;\r
+            height += annotationPanel.adjustPanelHeight()+3;\r
         }\r
 \r
         try\r

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index bc14d66..9bbcc24 100755 (executable)
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -76,6 +76,12 @@ public class AnnotationPanel extends JPanel implements MouseListener,
         ap.annotationScroller.getVerticalScrollBar().addAdjustmentListener(this);\r
     }\r
 \r
+    public AnnotationPanel(AlignViewport av)\r
+    {\r
+      this.av = av;\r
+    }\r
+\r
+\r
     /**\r
      * DOCUMENT ME!\r
      *\r
@@ -89,7 +95,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
     /**\r
      * DOCUMENT ME!\r
      */\r
-    public void adjustPanelHeight()\r
+    public int adjustPanelHeight()\r
     {\r
         // setHeight of panels\r
         image = null;\r
@@ -136,6 +142,8 @@ public class AnnotationPanel extends JPanel implements MouseListener,
         }\r
 \r
         this.setPreferredSize(new Dimension(1, height));\r
+\r
+        return height;\r
     }\r
 \r
     /**\r

diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index 9581ccc..2951c14 100755 (executable)
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -217,12 +217,28 @@ public class IdCanvas extends JPanel
 \r
         if (av.getWrapAlignment())\r
         {\r
+          int annotationHeight = 0;\r
+\r
+          if(av.showAnnotation)\r
+          {\r
+            AnnotationPanel ap = new AnnotationPanel(av);\r
+            annotationHeight = ap.adjustPanelHeight();\r
+          }\r
+\r
+          int hgap = av.charHeight;\r
+          if (av.scaleAboveWrapped)\r
+            hgap += av.charHeight;\r
+\r
+          int cHeight = av.getAlignment().getHeight() * av.charHeight\r
+              + hgap\r
+              + annotationHeight;\r
+\r
             int rowSize = av.getEndRes() - av.getStartRes();\r
 \r
             // Draw the rest of the panels\r
-            for (int ypos = 2 * av.charHeight, row = av.startRes;\r
+            for (int ypos = hgap, row = av.startRes;\r
                     (ypos <= getHeight()) && (row < av.alignment.getWidth());\r
-                    ypos += av.chunkHeight, row += rowSize)\r
+                    ypos += cHeight, row += rowSize)\r
             {\r
                 for (int i = starty; i < av.alignment.getHeight(); i++)\r
                 {\r

diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index 201516f..011502b 100755 (executable)
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -70,6 +70,16 @@ public class IdPanel extends JPanel implements MouseListener,
     {\r
     }\r
 \r
+    int getWrappedY(int y)\r
+    {\r
+      int hgap = av.charHeight;\r
+      if (av.scaleAboveWrapped)\r
+        hgap += av.charHeight;\r
+\r
+      return y - hgap;\r
+    }\r
+\r
+\r
     /**\r
      * DOCUMENT ME!\r
      *\r
@@ -83,7 +93,7 @@ public class IdPanel extends JPanel implements MouseListener,
 \r
         if (av.getWrapAlignment())\r
         {\r
-            y -= (2 * av.charHeight);\r
+            y = getWrappedY(y);\r
         }\r
 \r
         int seq = av.getIndex(y);\r
@@ -125,7 +135,7 @@ public class IdPanel extends JPanel implements MouseListener,
 \r
       if (av.getWrapAlignment())\r
       {\r
-        y -= (2 * av.charHeight);\r
+         y = getWrappedY(y);\r
       }\r
 \r
       //DEFAULT LINK IS FIRST IN THE LINK LIST\r
@@ -205,7 +215,7 @@ public class IdPanel extends JPanel implements MouseListener,
 \r
         if (av.getWrapAlignment())\r
         {\r
-            y -= (2 * av.charHeight);\r
+            y = getWrappedY(y);\r
         }\r
 \r
         int seq = av.getIndex(y);\r

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 1ed5e50..303aac6 100755 (executable)
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -43,8 +43,6 @@ public class SeqCanvas extends JComponent
     AlignViewport av;\r
     boolean displaySearch = false;\r
     int[] searchResults = null;\r
-    int chunkHeight;\r
-    int chunkWidth;\r
     boolean fastPaint = false;\r
     int LABEL_WEST;\r
     int LABEL_EAST;\r
@@ -294,11 +292,6 @@ public class SeqCanvas extends JComponent
         gg.setColor(Color.white);\r
         gg.fillRect(0, 0, imgWidth, imgHeight);\r
 \r
-        chunkWidth = getWrappedCanvasWidth(getWidth());\r
-        chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;\r
-\r
-        av.setChunkHeight(chunkHeight);\r
-        av.setChunkWidth(chunkWidth);\r
 \r
         if (av.getWrapAlignment())\r
         {\r
@@ -385,13 +378,21 @@ public class SeqCanvas extends JComponent
             LABEL_WEST = fm.stringWidth(getMask());\r
         }\r
 \r
+        int hgap = av.charHeight;\r
+        if(av.scaleAboveWrapped)\r
+          hgap += av.charHeight;\r
+\r
         int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth;\r
-        int cHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;\r
+        int cHeight = av.getAlignment().getHeight() * av.charHeight;\r
+\r
+        av.setWrappedWidth(cWidth);\r
 \r
         av.endRes = av.startRes + cWidth;\r
 \r
+\r
         int endx = (startRes + cWidth) - 1;\r
-        int ypos = 2 * av.charHeight;\r
+        int ypos = hgap;\r
+\r
 \r
         while ((ypos <= canvasHeight) && (startRes < av.alignment.getWidth()))\r
         {\r
@@ -437,10 +438,23 @@ public class SeqCanvas extends JComponent
 \r
 \r
             drawPanel(g, startRes, endx, 0, al.getHeight(), startRes, 0, ypos);\r
+\r
+            if(av.showAnnotation)\r
+            {\r
+              g.translate(0, cHeight + ypos + 3);\r
+              if(annotations==null)\r
+                annotations = new AnnotationPanel(av);\r
+\r
+              annotations.drawComponent( (Graphics2D) g, startRes, endx + 1);\r
+              g.translate(0, -cHeight - ypos);\r
+            }\r
             g.setClip(clip);\r
             g.translate(-LABEL_WEST, 0);\r
 \r
-            ypos += cHeight;\r
+            ypos += cHeight+getAnnotationHeight()+hgap;\r
+            if(av.showAnnotation)\r
+              ypos -= 3;\r
+\r
             startRes += cWidth;\r
             endx = (startRes + cWidth) - 1;\r
 \r
@@ -451,6 +465,18 @@ public class SeqCanvas extends JComponent
         }\r
     }\r
 \r
+    AnnotationPanel annotations;\r
+    int getAnnotationHeight()\r
+    {\r
+      if(!av.showAnnotation)\r
+        return 0;\r
+\r
+      if(annotations==null)\r
+        annotations = new AnnotationPanel(av);\r
+\r
+      return annotations.adjustPanelHeight();\r
+    }\r
+\r
     /**\r
      * DOCUMENT ME!\r
      *\r

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 8146be0..8486ac1 100755 (executable)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -212,16 +212,26 @@ public class SeqPanel extends JPanel
 \r
     if (av.wrapAlignment)\r
     {\r
+\r
+      int hgap = av.charHeight;\r
+      if (av.scaleAboveWrapped)\r
+        hgap += av.charHeight;\r
+\r
+      int cHeight = av.getAlignment().getHeight() * av.charHeight\r
+          + hgap + seqCanvas.getAnnotationHeight();\r
+\r
         int y = evt.getY();\r
-        y -= (2 * av.charHeight);\r
+        y -= hgap;\r
         x -= seqCanvas.LABEL_WEST;\r
 \r
-        int chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;\r
+\r
         int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());\r
-        wrappedBlock = y/chunkHeight;\r
-        wrappedBlock += av.getStartRes()/cwidth;\r
 \r
-        res = wrappedBlock*cwidth   +   x / av.getCharWidth();\r
+        wrappedBlock = y / cHeight;\r
+        wrappedBlock += av.getStartRes() / cwidth;\r
+\r
+        res = wrappedBlock * cwidth + x / av.getCharWidth();\r
+\r
     }\r
     else\r
     {\r
@@ -234,14 +244,22 @@ public class SeqPanel extends JPanel
 \r
    int findSeq(MouseEvent evt)\r
    {\r
+\r
      int seq = 0;\r
      int y = evt.getY();\r
 \r
      if (av.wrapAlignment)\r
      {\r
-       y -= (2 * av.charHeight);\r
-       int chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;\r
-       seq = ( (y % chunkHeight) / av.getCharHeight());\r
+       int hgap = av.charHeight;\r
+       if (av.scaleAboveWrapped)\r
+         hgap += av.charHeight;\r
+\r
+       int cHeight = av.getAlignment().getHeight() * av.charHeight\r
+           + hgap + seqCanvas.getAnnotationHeight();\r
+\r
+         y -= hgap;\r
+\r
+       seq = ( (y % cHeight) / av.getCharHeight());\r
      }\r
      else\r
      {\r
@@ -602,8 +620,18 @@ public class SeqPanel extends JPanel
 \r
       startWrapBlock=wrappedBlock;\r
 \r
-      if(seq<0 || res<0)\r
+      if(av.wrapAlignment && seq>av.alignment.getHeight())\r
+      {\r
+          JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+              "Cannot edit annotations in wrapped view.",\r
+              "Wrapped view - no edit",\r
+              JOptionPane.WARNING_MESSAGE);\r
         return;\r
+      }\r
+\r
+      if(seq<0 || res<0)\r
+            return;\r
+\r
 \r
         SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);\r
 \r

diff --git a/src/jalview/io/HTMLOutput.java b/src/jalview/io/HTMLOutput.java
index e4dc83e..08eacd6 100755 (executable)
--- a/src/jalview/io/HTMLOutput.java
+++ b/src/jalview/io/HTMLOutput.java
@@ -205,9 +205,9 @@ public class HTMLOutput
         "<table border=\"0\"  cellpadding=\"0\" cellspacing=\"0\">\n");\r
 \r
     for (int startRes = 0; startRes < al.getWidth();\r
-         startRes += av.getChunkWidth())\r
+         startRes += av.getWrappedWidth())\r
     {\r
-      int endRes = startRes + av.getChunkWidth();\r
+      int endRes = startRes + av.getWrappedWidth();\r
 \r
       if (endRes > al.getWidth())\r
       {\r