image is panel size
[jalview.git] / src / jalview / appletgui / AnnotationPanel.java
index 2cf5beb..172211e 100755 (executable)
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
+ */\r
+\r
 package jalview.appletgui;\r
 \r
-import jalview.datamodel.*;\r
+import java.util.*;\r
 \r
 import java.awt.*;\r
 import java.awt.event.*;\r
-import java.util.*;\r
 \r
-public class AnnotationPanel extends Panel implements AdjustmentListener\r
+import jalview.datamodel.*;\r
+\r
+public class AnnotationPanel\r
+    extends Panel implements AdjustmentListener\r
 {\r
   AlignViewport av;\r
   AlignmentPanel ap;\r
-  int activeRow =-1;\r
+  int activeRow = -1;\r
 \r
   Vector activeRes;\r
-  static String HELIX ="Helix";\r
-  static String SHEET ="Sheet";\r
-  static String LABEL ="Label";\r
-  static String REMOVE="Remove Annotation";\r
-  static String COLOUR="Colour";\r
+  static String HELIX = "Helix";\r
+  static String SHEET = "Sheet";\r
+  static String LABEL = "Label";\r
+  static String REMOVE = "Remove Annotation";\r
+  static String COLOUR = "Colour";\r
   static Color HELIX_COLOUR = Color.red.darker();\r
   static Color SHEET_COLOUR = Color.green.darker().darker();\r
 \r
-\r
   Image image;\r
   Graphics gg;\r
   FontMetrics fm;\r
-  int imgWidth=0;\r
+  int imgWidth = 0;\r
 \r
   boolean fastPaint = false;\r
 \r
   public static int GRAPH_HEIGHT = 40;\r
 \r
-\r
+  boolean MAC = false;\r
 \r
   public AnnotationPanel(AlignmentPanel ap)\r
   {\r
+    if (System.getProperty("os.name").startsWith("Mac"))\r
+      MAC = true;\r
+\r
     this.ap = ap;\r
     av = ap.av;\r
-    this.setLayout(null);\r
+    setLayout(null);\r
     adjustPanelHeight();\r
 \r
     addMouseMotionListener(new MouseMotionAdapter()\r
-    {public void mouseMoved(MouseEvent evt)\r
-          { doMouseMoved(evt); }\r
+    {\r
+      public void mouseMoved(MouseEvent evt)\r
+      {\r
+        doMouseMoved(evt);\r
+      }\r
     });\r
 \r
-   // ap.annotationScroller.getVAdjustable().addAdjustmentListener( this );\r
+    // ap.annotationScroller.getVAdjustable().addAdjustmentListener( this );\r
   }\r
 \r
+\r
+  public AnnotationPanel(AlignViewport av)\r
+  {\r
+    this.av = av;\r
+  }\r
+\r
+\r
   public void adjustmentValueChanged(AdjustmentEvent evt)\r
   {\r
-    ap.alabels.setScrollOffset( -evt.getValue() );\r
+    ap.alabels.setScrollOffset( -evt.getValue());\r
   }\r
 \r
-  public void adjustPanelHeight()\r
+  public int adjustPanelHeight()\r
   {\r
     // setHeight of panels\r
     AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
+\r
+\r
     int height = 0;\r
-    if(aa!=null)\r
-    for (int i = 0; i < aa.length; i++)\r
+    if (aa != null)\r
     {\r
-      if(!aa[i].visible)\r
-        continue;\r
+      for (int i = 0; i < aa.length; i++)\r
+      {\r
+        if (!aa[i].visible)\r
+        {\r
+          continue;\r
+        }\r
 \r
-      aa[i].height = 0;\r
+        aa[i].height = 0;\r
 \r
-      if(aa[i].hasText)\r
-        aa[i].height += av.charHeight;\r
-      if (aa[i].hasIcons)\r
-        aa[i].height += 16;\r
+        if (aa[i].hasText)\r
+        {\r
+          aa[i].height += av.charHeight;\r
+        }\r
+        if (aa[i].hasIcons)\r
+        {\r
+          aa[i].height += 16;\r
+        }\r
 \r
-      if (aa[i].isGraph)\r
-        aa[i].height += GRAPH_HEIGHT;\r
+        if (aa[i].graph>0)\r
+        {\r
+          aa[i].height += GRAPH_HEIGHT;\r
+        }\r
 \r
-      if(aa[i].height==0)\r
-        aa[i].height = 20;\r
-      height += aa[i].height;\r
+        if (aa[i].height == 0)\r
+        {\r
+          aa[i].height = 20;\r
+        }\r
+        height += aa[i].height;\r
+      }\r
+    }\r
+    else\r
+    {\r
+      height = 20;\r
     }\r
-  else height=20;\r
 \r
-   this.setSize(getSize().width, height);\r
-   ap.annotationScroller.setSize(getSize().width, height);\r
+    this.setSize(getSize().width, height);\r
 \r
-//  ap.annotationSpaceFillerHolder.setSize(d.width,annotationPanel.getSize().height);\r
+    repaint();\r
 \r
-   repaint();\r
+    return height;\r
 \r
   }\r
 \r
   public void addEditableColumn(int i)\r
   {\r
-    if(activeRow==-1)\r
+    if (activeRow == -1)\r
     {\r
-      AlignmentAnnotation [] aa = av.alignment.getAlignmentAnnotation();\r
-      for(int j=0; j<aa.length; j++)\r
-        if(aa[j].editable)\r
+      AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
+      if(aa ==null)\r
+        return;\r
+\r
+      for (int j = 0; j < aa.length; j++)\r
+      {\r
+        if (aa[j].editable)\r
         {\r
           activeRow = j;\r
           break;\r
         }\r
+      }\r
     }\r
 \r
-    if(activeRes==null)\r
+    if (activeRes == null)\r
     {\r
       activeRes = new Vector();\r
       activeRes.addElement(String.valueOf(i));\r
@@ -112,38 +166,44 @@ public class AnnotationPanel extends Panel implements AdjustmentListener
     activeRes.addElement(String.valueOf(i));\r
   }\r
 \r
- public void doMouseMoved(MouseEvent evt)\r
- {\r
-   AlignmentAnnotation [] aa = av.alignment.getAlignmentAnnotation();\r
-   if(aa==null)\r
-     return;\r
+  public void doMouseMoved(MouseEvent evt)\r
+  {\r
+    AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
+    if (aa == null)\r
+    {\r
+      return;\r
+    }\r
 \r
-   int row = -1;\r
-   int height=0;\r
-   for(int i=0; i<aa.length; i++)\r
-   {\r
+    int row = -1;\r
+    int height = 0;\r
+    for (int i = 0; i < aa.length; i++)\r
+    {\r
 \r
-     if( aa[i].visible )\r
-       height += aa[i].height;\r
+      if (aa[i].visible)\r
+      {\r
+        height += aa[i].height;\r
+      }\r
 \r
-     if(evt.getY()<height)\r
-     {\r
-       row = i;\r
-       break;\r
-     }\r
-   }\r
+      if (evt.getY() < height)\r
+      {\r
+        row = i;\r
+        break;\r
+      }\r
+    }\r
 \r
-   int res = evt.getX() / av.getCharWidth() + av.getStartRes();\r
-   if(row>-1 && res<aa[row].annotations.length && aa[row].annotations[res]!=null)\r
-   {\r
-     StringBuffer text = new StringBuffer("Sequence position " + (res + 1) +\r
-                                          "  " +\r
-                                          aa[row].annotations[res].description);\r
-     ap.alignFrame.statusBar.setText(text.toString());\r
-   }\r
- }\r
+    int res = evt.getX() / av.getCharWidth() + av.getStartRes();\r
 \r
+    if(av.hasHiddenColumns)\r
+          res = av.getColumnSelection().adjustForHiddenColumns(res);\r
 \r
+        if (row > -1 && res < aa[row].annotations.length && aa[row].annotations[res] != null)\r
+        {\r
+          StringBuffer text = new StringBuffer("Sequence position " + (res + 1));\r
+          if (aa[row].annotations[res].description != null)\r
+            text.append("  " + aa[row].annotations[res].description);\r
+          ap.alignFrame.statusBar.setText(text.toString());\r
+        }\r
+  }\r
 \r
   public void update(Graphics g)\r
   {\r
@@ -152,258 +212,570 @@ public class AnnotationPanel extends Panel implements AdjustmentListener
 \r
   public void paint(Graphics g)\r
   {\r
-    imgWidth = (av.endRes-av.startRes+1) *av.charWidth;\r
 \r
-    if(image==null || imgWidth != image.getWidth(this))\r
-      {\r
-        image = createImage(imgWidth, ap.annotationPanel.getSize().height);\r
-        gg = image.getGraphics();\r
-        gg.setFont(av.getFont());\r
-        fm = gg.getFontMetrics();\r
-        fastPaint = false;\r
+    imgWidth = getSize().width;\r
+        //(av.endRes - av.startRes + 1) * av.charWidth;\r
+\r
+    if (image == null || imgWidth != image.getWidth(this))\r
+    {\r
+      image = createImage(imgWidth, ap.annotationPanel.getSize().height);\r
+      gg = image.getGraphics();\r
+      gg.setFont(av.getFont());\r
+      fm = gg.getFontMetrics();\r
+      fastPaint = false;\r
     }\r
 \r
-    if(fastPaint)\r
+    if (fastPaint)\r
     {\r
       g.drawImage(image, 0, 0, this);\r
       fastPaint = false;\r
       return;\r
     }\r
 \r
-    drawComponent( gg, av.startRes, av.endRes+1);\r
-    g.drawImage( image, 0, 0, this);\r
-\r
+    drawComponent(gg, av.startRes, av.endRes + 1);\r
+    g.drawImage(image, 0, 0, this);\r
   }\r
 \r
   public void fastPaint(int horizontal)\r
-{\r
-  if( horizontal == 0\r
-     || av.alignment.getAlignmentAnnotation()==null\r
-     || av.alignment.getAlignmentAnnotation().length<1\r
-    )\r
   {\r
+    if (horizontal == 0\r
+        || av.alignment.getAlignmentAnnotation() == null\r
+        || av.alignment.getAlignmentAnnotation().length < 1\r
+        )\r
+    {\r
+      repaint();\r
+      return;\r
+    }\r
+\r
+    gg.copyArea(0, 0, imgWidth, getSize().height, -horizontal * av.charWidth, 0);\r
+    int sr = av.startRes, er = av.endRes + 1, transX = 0;\r
+\r
+    if (horizontal > 0) // scrollbar pulled right, image to the left\r
+    {\r
+      transX = (er - sr - horizontal) * av.charWidth;\r
+      sr = er - horizontal;\r
+    }\r
+    else if (horizontal < 0)\r
+    {\r
+      er = sr - horizontal;\r
+    }\r
+\r
+    gg.translate(transX, 0);\r
+\r
+    drawComponent(gg, sr, er);\r
+\r
+    gg.translate( -transX, 0);\r
+\r
+    fastPaint = true;\r
     repaint();\r
-    return;\r
   }\r
 \r
-  gg.copyArea( 0,0, imgWidth, getSize().height, -horizontal*av.charWidth, 0 );\r
-  int sr=av.startRes, er=av.endRes+1, transX=0;\r
-\r
-  if(horizontal>0) // scrollbar pulled right, image to the left\r
+  /**\r
+   * DOCUMENT ME!\r
+   *\r
+   * @param g DOCUMENT ME!\r
+   * @param startRes DOCUMENT ME!\r
+   * @param endRes DOCUMENT ME!\r
+   */\r
+  public void drawComponent(Graphics g, int startRes, int endRes)\r
   {\r
-    transX =  (er-sr-horizontal)*av.charWidth;\r
-    sr = er - horizontal ;\r
+    g.setFont(av.getFont());\r
+\r
+    if (fm == null)\r
+      fm = g.getFontMetrics();\r
+\r
+\r
+      g.setColor(Color.white);\r
+      g.fillRect(0, 0, getSize().width, getSize().height);\r
+\r
+      if ((av.alignment.getAlignmentAnnotation() == null) ||\r
+              (av.alignment.getAlignmentAnnotation().length < 1))\r
+      {\r
+          g.setColor(Color.white);\r
+          g.fillRect(0, 0, getSize().width, getSize().height);\r
+          g.setColor(Color.black);\r
+          if(av.validCharWidth)\r
+            g.drawString("Alignment has no annotations", 20, 15);\r
+\r
+          return;\r
+      }\r
+\r
+      AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
+\r
+      int x = 0;\r
+      int y = 0;\r
+      int column=0;\r
+      char lastSS;\r
+      int lastSSX;\r
+      int iconOffset = av.charHeight / 2;\r
+      boolean validRes = false;\r
+\r
+      boolean [] graphGroupDrawn = new boolean[aa.length];\r
+\r
+\r
+      //\u03B2 \u03B1\r
+      for (int i = 0; i < aa.length; i++)\r
+      {\r
+          AlignmentAnnotation row = aa[i];\r
+\r
+          if (!row.visible)\r
+          {\r
+              continue;\r
+          }\r
+\r
+          lastSS = ' ';\r
+          lastSSX = 0;\r
+\r
+          if (row.graph>0)\r
+          {\r
+              if(row.graphGroup>-1 && graphGroupDrawn[ row.graphGroup ] )\r
+                continue;\r
+\r
+              // this is so that we draw the characters below the graph\r
+              y += row.height;\r
+\r
+              if (row.hasText)\r
+              {\r
+                  y -= av.charHeight;\r
+              }\r
+          }\r
+\r
+          if (row.hasText)\r
+          {\r
+              iconOffset = av.charHeight / 2;\r
+          }\r
+          else\r
+          {\r
+              iconOffset = 0;\r
+          }\r
+\r
+           x = 0;\r
+          while(x < endRes-startRes)\r
+          {\r
+            if (av.hasHiddenColumns)\r
+            {\r
+              column = av.getColumnSelection().adjustForHiddenColumns(startRes+x);\r
+              if (column > row.annotations.length-1)\r
+              {\r
+                break;\r
+              }\r
+            }\r
+            else\r
+                column = startRes+x;\r
+\r
+              if ( (row.annotations.length <= column) ||\r
+                  (row.annotations[column] == null))\r
+              {\r
+                validRes = false;\r
+              }\r
+              else\r
+              {\r
+                validRes = true;\r
+              }\r
+\r
+\r
+              if (av.validCharWidth && validRes &&\r
+                        (row.annotations[column].displayCharacter.length() > 0))\r
+              {\r
+                int charOffset = (av.charWidth -\r
+                    fm.charWidth(row.annotations[column].displayCharacter.charAt(\r
+                            0))) / 2;\r
+                g.setColor(row.annotations[column].colour);\r
+\r
+                if (column == 0 || row.graph>0)\r
+                {\r
+                    g.drawString(row.annotations[column].displayCharacter,\r
+                                (x*av.charWidth)+charOffset,\r
+                        y + iconOffset + 3);\r
+                }\r
+                else if (\r
+                    row.annotations[column - 1] == null\r
+                    ||(!row.annotations[column].displayCharacter.equals(\r
+                        row.annotations[column - 1].displayCharacter)\r
+                    ||\r
+              (row.annotations[column].displayCharacter.length() <2 &&\r
+               row.annotations[column].secondaryStructure==' ')))\r
+                {\r
+                    g.drawString(row.annotations[column].displayCharacter,\r
+                       (x*av.charWidth)+charOffset,\r
+                        y + iconOffset + 3);\r
+                    }\r
+              }\r
+\r
+              if (row.hasIcons)\r
+              {\r
+                  if (!validRes ||\r
+                          (row.annotations[column].secondaryStructure != lastSS))\r
+                  {\r
+                      switch (lastSS)\r
+                      {\r
+                      case 'H':\r
+                        g.setColor(HELIX_COLOUR);\r
+                        if (MAC)\r
+                        {\r
+                          //Off by 1 offset when drawing rects and ovals\r
+                          //to offscreen image on the MAC\r
+                          g.fillRoundRect(lastSSX, y + 4 + iconOffset,\r
+                                          (x*av.charWidth) - lastSSX, 7, 8, 8);\r
+                          break;\r
+                        }\r
+\r
+                        int sCol = (lastSSX / av.charWidth) + startRes;\r
+                        int x1 = lastSSX;\r
+                        int x2 = (x*av.charWidth);\r
+\r
+                       if(sCol==0 ||\r
+                          row.annotations[sCol-1]==null ||\r
+                          row.annotations[sCol-1].secondaryStructure!='H')\r
+                       {\r
+                         g.fillArc(lastSSX, y+4+iconOffset, av.charWidth, 8, 90,180) ;\r
+                         x1 += av.charWidth/2;\r
+                       }\r
+\r
+                        if(row.annotations[column]==null ||\r
+                           row.annotations[column].secondaryStructure!='H')\r
+                        {\r
+                          g.fillArc((x*av.charWidth)-av.charWidth,\r
+                                    y+4+iconOffset, av.charWidth, 8, 270,180);\r
+                          x2 -= av.charWidth/2;\r
+                        }\r
+\r
+                        g.fillRect(x1, y+4+iconOffset, x2-x1, 8);\r
+                            break;\r
+\r
+                      case 'E':\r
+                          g.setColor(SHEET_COLOUR);\r
+                          g.fillRect(lastSSX, y + 4 + iconOffset,\r
+                              (x*av.charWidth) - lastSSX - 4, 7);\r
+                          g.fillPolygon(new int[] { (x*av.charWidth) - 4,\r
+                                        (x*av.charWidth) - 4,\r
+                                        (x*av.charWidth) },\r
+                              new int[]\r
+                              {\r
+                                  y + iconOffset, y + 14 + iconOffset,\r
+                                  y + 8 + iconOffset\r
+                              }, 3);\r
+\r
+                          break;\r
+\r
+\r
+                      default:\r
+                          g.setColor(Color.gray);\r
+                          g.fillRect(lastSSX, y + 6 + iconOffset,\r
+                              (x*av.charWidth) - lastSSX, 2);\r
+\r
+                          break;\r
+                      }\r
+\r
+                      if (validRes)\r
+                      {\r
+                          lastSS = row.annotations[column].secondaryStructure;\r
+                      }\r
+                      else\r
+                      {\r
+                          lastSS = ' ';\r
+                      }\r
+\r
+                      lastSSX = (x*av.charWidth);\r
+                  }\r
+              }\r
+\r
+\r
+          column++;\r
+          x++;\r
+          }\r
+\r
+          if(column>=row.annotations.length)\r
+              column = row.annotations.length-1;\r
+\r
+        //  x ++;\r
+\r
+          if (row.hasIcons)\r
+          {\r
+            switch (lastSS)\r
+            {\r
+              case 'H':\r
+                g.setColor(HELIX_COLOUR);\r
+                if (MAC)\r
+                {\r
+                  //Off by 1 offset when drawing rects and ovals\r
+                  //to offscreen image on the MAC\r
+                  g.fillRoundRect(lastSSX, y + 4 + iconOffset,\r
+                                  (x*av.charWidth) - lastSSX, 7, 8, 8);\r
+                  break;\r
+                }\r
+\r
+                int sCol = (lastSSX / av.charWidth) + startRes;\r
+                int x1 = lastSSX;\r
+                int x2 = (x*av.charWidth);\r
+\r
+                if (sCol == 0 ||\r
+                    row.annotations[sCol - 1] == null ||\r
+                    row.annotations[sCol - 1].secondaryStructure != 'H')\r
+                {\r
+                  g.fillArc(lastSSX, y + 4 + iconOffset, av.charWidth, 8, 90, 180);\r
+                  x1 += av.charWidth / 2;\r
+                }\r
+\r
+                if (row.annotations[column] == null ||\r
+                    row.annotations[column].secondaryStructure != 'H')\r
+                {\r
+                  g.fillArc((x*av.charWidth) - av.charWidth,\r
+                            y + 4 + iconOffset, av.charWidth, 8, 270,\r
+                            180);\r
+                  x2 -= av.charWidth / 2;\r
+                }\r
+\r
+                g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);\r
+\r
+                break;\r
+\r
+              case 'E':\r
+                g.setColor(SHEET_COLOUR);\r
+\r
+                if (row.annotations[endRes] == null\r
+                    || row.annotations[endRes].secondaryStructure != 'E')\r
+                {\r
+                  g.fillRect(lastSSX, y + 4 + iconOffset,\r
+                             (x*av.charWidth) - lastSSX - 4, 7);\r
+                  g.fillPolygon(new int[]\r
+                                {(x*av.charWidth) - 4,\r
+                                (x*av.charWidth) - 4,\r
+                               (x*av.charWidth)},\r
+                                new int[]\r
+                                {\r
+                                y + iconOffset, y + 14 + iconOffset,\r
+                                y + 7 + iconOffset\r
+                  }, 3);\r
+                }\r
+                else\r
+                 {\r
+                   g.fillRect(lastSSX, y + 4 + iconOffset,\r
+                              x * av.charWidth - lastSSX, 7);\r
+                 }\r
+                break;\r
+\r
+              default:\r
+                g.setColor(Color.gray);\r
+                if(!av.wrapAlignment || endRes==av.endRes)\r
+                g.fillRect(lastSSX, y + 6 + iconOffset,\r
+                           (x*av.charWidth) - lastSSX, 2);\r
+\r
+                break;\r
+            }\r
+          }\r
+\r
+          if (row.graph>0)\r
+          {\r
+              if(row.graph == AlignmentAnnotation.LINE_GRAPH )\r
+              {\r
+                if(row.graphGroup>-1 && !graphGroupDrawn[row.graphGroup])\r
+                 {\r
+                   float groupmax=-999999, groupmin=9999999;\r
+                   for(int gg=0; gg<aa.length; gg++)\r
+                   {\r
+                     if(aa[gg].graphGroup!=row.graphGroup)\r
+                       continue;\r
+\r
+                     if(aa[gg]!=row)\r
+                       aa[gg].visible = false;\r
+\r
+                     if(aa[gg].graphMax>groupmax)\r
+                       groupmax = aa[gg].graphMax;\r
+                     if(aa[gg].graphMin<groupmin)\r
+                       groupmin = aa[gg].graphMin;\r
+                   }\r
+\r
+                   for (int gg = 0; gg < aa.length; gg++)\r
+                   {\r
+                     if (aa[gg].graphGroup == row.graphGroup)\r
+                     {\r
+                       drawLineGraph(g, aa[gg], startRes, endRes, y,\r
+                                     groupmin, groupmax,\r
+                                     row.graphHeight);\r
+                     }\r
+                   }\r
+\r
+                   graphGroupDrawn[ row.graphGroup ] = true;\r
+                 }\r
+                 else\r
+                   drawLineGraph(g, row, startRes, endRes,\r
+                                 y, row.graphMin, row.graphMax, row.graphHeight  );\r
+              }\r
+              else if(row.graph == AlignmentAnnotation.BAR_GRAPH )\r
+                 drawBarGraph(g, row, startRes, endRes,\r
+                              row.graphMin, row.graphMax, y);\r
+          }\r
+\r
+          if (row.graph>0 && row.hasText)\r
+          {\r
+              y += av.charHeight;\r
+          }\r
+\r
+          if (row.graph==0)\r
+          {\r
+              y += aa[i].height;\r
+          }\r
+      }\r
   }\r
-  else if(horizontal<0)\r
+\r
+  public void drawLineGraph(Graphics g, AlignmentAnnotation aa,\r
+                            int sRes, int eRes,\r
+                            int y,\r
+                            float min, float max,\r
+                            int graphHeight)\r
   {\r
-    er = sr-horizontal;\r
-  }\r
+    if(sRes>aa.annotations.length)\r
+      return;\r
 \r
 \r
-  gg.translate(transX, 0);\r
 \r
-  drawComponent(gg, sr, er);\r
+    int x = 0;\r
 \r
-  gg.translate( -transX, 0 );\r
+    //Adjustment for fastpaint to left\r
+    if(eRes<av.endRes)\r
+      eRes++;\r
 \r
-  fastPaint = true;\r
-  repaint();\r
-}\r
+    eRes = Math.min(eRes, aa.annotations.length);\r
 \r
 \r
-  public void drawComponent(Graphics g, int startRes, int endRes)\r
-  {\r
-    g.setColor(Color.white);\r
-    g.fillRect(0,0,(endRes-startRes) *av.charWidth, getSize().height);\r
-    if(av.alignment.getAlignmentAnnotation()==null || av.alignment.getAlignmentAnnotation().length<1)\r
+    if(sRes==0)\r
     {\r
-      g.setColor(Color.white);\r
-      g.fillRect(0,0,getSize().width, getSize().height);\r
-      g.setColor(Color.black);\r
-      g.drawString("Alignment has no annotations",20,15);\r
-      return;\r
+      sRes++;\r
+      x+=av.charWidth;\r
     }\r
 \r
-    AlignmentAnnotation [] aa = av.alignment.getAlignmentAnnotation();\r
+    int y1=y, y2=y;\r
+    float range = max - min;\r
 \r
-    int j, x=0, y=0;\r
-    char [] lastSS = new char[aa.length];\r
-    int  [] lastSSX= new int[aa.length] ;\r
-    int iconOffset = av.charHeight/2;\r
-    boolean validRes = false;\r
-    //\u03B2 \u03B1\r
+    ////Draw origin\r
+    if(min<0)\r
+      y2 = y - (int)((0-min / range)*graphHeight);\r
 \r
-    for(int i=0; i<aa.length; i++)\r
-    {\r
-      AlignmentAnnotation row = aa[i];\r
-      if(!row.visible)\r
-        continue;\r
+    g.setColor(Color.gray);\r
+    g.drawLine(x-av.charWidth,y2,(eRes-sRes)*av.charWidth,y2);\r
+\r
+    eRes = Math.min(eRes, aa.annotations.length);\r
 \r
-      if(row.isGraph)\r
+    int column;\r
+    int aaMax = aa.annotations.length-1;\r
+\r
+    while( x < eRes - sRes )\r
+    {\r
+      column = sRes + x;\r
+      if(av.hasHiddenColumns)\r
       {\r
-        // this is so that we draw the characters below the graph\r
-        y += row.height;\r
-        if(row.hasText)\r
-          y -= av.charHeight;\r
+        column = av.getColumnSelection().adjustForHiddenColumns(column);\r
       }\r
-      if(row.hasText)\r
-        iconOffset = av.charHeight/2;\r
-      else\r
-        iconOffset = 0;\r
 \r
-      for(j=startRes; j<endRes; j++)\r
+      if (column > aaMax)\r
       {\r
-        if(row.annotations.length<=j || row.annotations[j]==null)\r
-        validRes = false;\r
-       else\r
-         validRes = true;\r
-\r
-       x = (j-startRes)*av.charWidth;\r
+        break;\r
+      }\r
 \r
+      if(aa.annotations[column]==null || aa.annotations[column-1]==null)\r
+      {\r
+        x++;\r
+        continue;\r
+      }\r
 \r
-       if(activeRow==i)\r
-       {\r
+        g.setColor(aa.annotations[column].colour);\r
+        y1 = y - (int) (((aa.annotations[column-1].value-min) / range) * graphHeight);\r
+        y2 = y - (int) (((aa.annotations[column].value-min) / range) * graphHeight);\r
 \r
-         g.setColor(Color.red);\r
+        g.drawLine(x*av.charWidth-av.charWidth/2, y1, x*av.charWidth+av.charWidth/2, y2);\r
+        x ++;\r
+     }\r
 \r
-         if(activeRes!=null)\r
-           for (int n = 0; n < activeRes.size(); n++)\r
-           {\r
-             int v = Integer.parseInt(activeRes.elementAt(n).toString()) ;\r
-             if (v == j)\r
-               g.fillRect( (j-startRes) * av.charWidth, y, av.charWidth, row.height);\r
-           }\r
-       }\r
+     if(aa.threshold!=null)\r
+     {\r
+         g.setColor(aa.threshold.colour);\r
 \r
+         y2 = (int)(y - ((aa.threshold.value-min) / range)*graphHeight);\r
+         g.drawLine(0,y2,(eRes-sRes)*av.charWidth,y2);\r
+    }\r
+  }\r
 \r
+  public void drawBarGraph(Graphics g, AlignmentAnnotation aa,\r
+                           int sRes, int eRes,\r
+                           float min, float max,\r
+                           int y)\r
+  {\r
+    if(sRes>aa.annotations.length)\r
+      return;\r
 \r
-       if(validRes && row.annotations[j].displayCharacter.length()>0)\r
-       {\r
-         int charOffset = (av.charWidth - fm.charWidth(row.annotations[j].displayCharacter.charAt(0)))/2;\r
-         g.setColor( row.annotations[j].colour);\r
-          if(j==0)\r
-          {\r
-            if (row.annotations[0].secondaryStructure == 'H'\r
-                || row.annotations[0].secondaryStructure == 'E')\r
-              g.drawString(row.annotations[j].displayCharacter, x,\r
-                           y + iconOffset + 2);\r
-          }\r
-         else if( (row.annotations[j].secondaryStructure=='H'\r
-               || row.annotations[j].secondaryStructure=='E') &&\r
-               (row.annotations[j-1]==null ||\r
-                row.annotations[j].secondaryStructure!=row.annotations[j-1].secondaryStructure))\r
-\r
-        g.drawString(row.annotations[j].displayCharacter, x, y + iconOffset + 2);\r
-\r
-        if(!row.hasIcons)\r
-            g.drawString(row.annotations[j].displayCharacter, x + charOffset,\r
-                         y + iconOffset + 2);\r
-       }\r
-\r
-       if(row.hasIcons)\r
-       if(!validRes || row.annotations[j].secondaryStructure!=lastSS[i])\r
-       {\r
-         switch (lastSS[i])\r
-         {\r
-           case 'H':\r
-             g.setColor(HELIX_COLOUR);\r
-             g.fillRoundRect(lastSSX[i], y+4 + iconOffset, x-lastSSX[i], 7, 8, 8);\r
-             break;\r
-           case 'E':\r
-             g.setColor(SHEET_COLOUR);\r
-             g.fillRect(lastSSX[i], y + 4 + iconOffset, x-lastSSX[i]-4, 7);\r
-             g.fillPolygon(new int[] {x - 4, x- 4, x }\r
-                           , new int[]{y+ iconOffset, y + 14+ iconOffset, y + 8+ iconOffset}, 3);\r
-             break;\r
-           case 'C':\r
-             break;\r
-           default :\r
-             g.setColor(Color.gray);\r
-             g.fillRect(lastSSX[i], y+6+ iconOffset, x-lastSSX[i], 2);\r
-             break;\r
-         }\r
-\r
-         if(validRes)\r
-           lastSS[i] = row.annotations[j].secondaryStructure;\r
-          else\r
-            lastSS[i] = ' ';\r
-         lastSSX[i] = x;\r
-       }\r
+    eRes = Math.min(eRes, aa.annotations.length);\r
 \r
-       if (validRes && row.isGraph)\r
-       {\r
-         g.setColor(new Color(0,0,180));\r
-         int height = (int)((row.annotations[j].value / row.graphMax)*GRAPH_HEIGHT);\r
+    int x=0, y1=y, y2=y;\r
 \r
-         if(row.windowLength>1)\r
-         {\r
-           int total =0;\r
-           for(int i2=j- (row.windowLength/2); i2<j+(row.windowLength/2); i2++)\r
-           {\r
-             if(i2<0 || i2>=av.alignment.getWidth())\r
-               continue;\r
+    float range = max - min;\r
 \r
-             total += row.annotations[i2].value;\r
-           }\r
+    if(min<0)\r
+      y2 = y - (int)((0-min / (range))*aa.graphHeight);\r
 \r
-           total/=row.windowLength;\r
-           height = (int)( (total / row.graphMax) *GRAPH_HEIGHT);\r
+    g.setColor(Color.gray);\r
 \r
-         }\r
-         g.setColor(row.annotations[j].colour);\r
-         g.fillRect(x, y-height, av.charWidth, height );\r
-       }\r
+    g.drawLine(x,y2,(eRes-sRes)*av.charWidth,y2);\r
 \r
+    int column;\r
+    int aaMax = aa.annotations.length-1;\r
 \r
+    while( x < eRes-sRes )\r
+    {\r
+      column = sRes + x;\r
+      if(av.hasHiddenColumns)\r
+      {\r
+        column = av.getColumnSelection().adjustForHiddenColumns(column);\r
       }\r
 \r
-      x+=av.charWidth;\r
-\r
-      if(row.hasIcons)\r
-      switch (lastSS[i])\r
+      if(column > aaMax)\r
       {\r
-        case 'H':\r
-          g.setColor(HELIX_COLOUR);\r
-          g.fillRoundRect(lastSSX[i], y+4+ iconOffset, x - lastSSX[i], 7, 8, 8);\r
-          break;\r
-        case 'E':\r
-          g.setColor(SHEET_COLOUR);\r
-          g.fillRect(lastSSX[i], y + 4+ iconOffset, x - lastSSX[i] - 4, 7);\r
-          g.fillPolygon(new int[]\r
-                        {x - 4, x - 4, x}\r
-                        , new int[]\r
-                        {y + iconOffset, y + 14+ iconOffset, y + 7+ iconOffset}\r
-                        , 3);\r
-          break;\r
-        case 'C':\r
-          break;\r
-        default:\r
-          g.setColor(Color.gray);\r
-          g.fillRect(lastSSX[i], y+6+ iconOffset, x-lastSSX[i], 2);\r
           break;\r
+      }\r
 \r
+      if (aa.annotations[column] == null)\r
+      {\r
+        x ++;\r
+        continue;\r
       }\r
 \r
-       if(row.isGraph && row.hasText)\r
-         y+=av.charHeight;\r
-       if(!row.isGraph)\r
-          y+=aa[i].height;\r
+        g.setColor(aa.annotations[column].colour);\r
+        y1 = y - (int) (((aa.annotations[column].value-min) / (range)) * aa.graphHeight);\r
+\r
+        if(y1-y2>0)\r
+          g.fillRect(x*av.charWidth, y2, av.charWidth, y1-y2 );\r
+        else\r
+          g.fillRect(x*av.charWidth, y1, av.charWidth, y2-y1 );\r
+\r
+        x ++ ;\r
+\r
     }\r
+    if(aa.threshold!=null)\r
+    {\r
+        g.setColor(aa.threshold.colour);\r
+        y2 = (int)(y - ((aa.threshold.value-min) / range)*aa.graphHeight);\r
+        g.drawLine(0,y2,(eRes-sRes)*av.charWidth,y2);\r
+      }\r
   }\r
 \r
   // used by overview window\r
-  public void drawGraph(Graphics g, AlignmentAnnotation aa,int width, int y)\r
+  public void drawGraph(Graphics g, AlignmentAnnotation aa, int width, int y, int sRes, int eRes)\r
   {\r
-    g.setColor(Color.white);\r
-    g.fillRect(0,0,width, y);\r
-    g.setColor(new Color(0,0,180));\r
-    int x = 0;\r
-    for(int j=0; j<aa.annotations.length; j++)\r
-    {\r
+      g.setColor(Color.white);\r
+      g.fillRect(0, 0, width, y);\r
       g.setColor(new Color(0, 0, 180));\r
-      int height = (int) ( (aa.annotations[j].value / aa.graphMax) * GRAPH_HEIGHT );\r
-      g.fillRect(x, y - height, av.charWidth, height);\r
-      x+=av.charWidth;\r
+\r
+      int x = 0, height;\r
+\r
+      for (int j = sRes; j < eRes; j++)\r
+      {\r
+          g.setColor(aa.annotations[j].colour);\r
+\r
+          height = (int) ((aa.annotations[j].value / aa.graphMax) * GRAPH_HEIGHT);\r
+          if(height>y)\r
+              height = y;\r
+          g.fillRect(x, y - height, av.charWidth, height);\r
+          x += av.charWidth;\r
+      }\r
     }\r
-  }\r
 }\r