/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\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
import java.awt.event.*;\r
import java.awt.image.*;\r
\r
-import java.util.*;\r
-\r
import javax.swing.*;\r
\r
\r
AlignViewport av;\r
AlignmentPanel ap;\r
int activeRow = -1;\r
- Vector activeRes;\r
BufferedImage image;\r
+ BufferedImage fadedImage;\r
Graphics2D gg;\r
FontMetrics fm;\r
int imgWidth = 0;\r
//Used For mouse Dragging and resizing graphs\r
int graphStretch = -1;\r
int graphStretchY = -1;\r
+ int min; //used by mouseDragged to see if user\r
+ int max; //used by mouseDragged to see if user\r
+ boolean mouseDragging = false;\r
+\r
+ boolean MAC = false;\r
\r
/**\r
* Creates a new AnnotationPanel object.\r
*/\r
public AnnotationPanel(AlignmentPanel ap)\r
{\r
+\r
+ if(System.getProperty("os.name").startsWith("Mac"))\r
+ MAC = true;\r
+\r
ToolTipManager.sharedInstance().registerComponent(this);\r
ToolTipManager.sharedInstance().setInitialDelay(0);\r
ToolTipManager.sharedInstance().setDismissDelay(10000);\r
return height;\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param col DOCUMENT ME!\r
- */\r
- public void removeEditableColumn(int col)\r
- {\r
- if (activeRow == -1)\r
- {\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
-\r
- break;\r
- }\r
- }\r
- }\r
-\r
- if ((activeRes != null) && activeRes.contains(String.valueOf(col)))\r
- {\r
- activeRes.removeElement(String.valueOf(col));\r
- }\r
-\r
- repaint();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param col DOCUMENT ME!\r
- */\r
- public void addEditableColumn(int col)\r
- {\r
- if (activeRow == -1)\r
- {\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
-\r
- break;\r
- }\r
- }\r
- }\r
-\r
- if (activeRes == null)\r
- {\r
- activeRes = new Vector();\r
- }\r
-\r
- if (!activeRes.contains(String.valueOf(col)))\r
- {\r
- activeRes.addElement(String.valueOf(col));\r
- }\r
-\r
- repaint();\r
- }\r
\r
/**\r
* DOCUMENT ME!\r
\r
if (evt.getActionCommand().equals(REMOVE))\r
{\r
- for (int i = 0; i < activeRes.size(); i++)\r
+ for (int i = 0; i < av.getColumnSelection().size(); i++)\r
{\r
- anot[Integer.parseInt(activeRes.get(i).toString())] = null;\r
- anot[Integer.parseInt(activeRes.get(i).toString())] = null;\r
+ anot[av.getColumnSelection().columnAt(i)] = null;\r
}\r
}\r
else if (evt.getActionCommand().equals(LABEL))\r
aa[activeRow].hasText = true;\r
}\r
\r
- for (int i = 0; i < activeRes.size(); i++)\r
+ for (int i = 0; i < av.getColumnSelection().size(); i++)\r
{\r
- int index = Integer.parseInt(activeRes.get(i).toString());\r
+ int index = av.getColumnSelection().columnAt(i);\r
\r
if (anot[index] == null)\r
{\r
Color col = JColorChooser.showDialog(this,\r
"Choose foreground colour", Color.black);\r
\r
- for (int i = 0; i < activeRes.size(); i++)\r
+ for (int i = 0; i < av.getColumnSelection().size(); i++)\r
{\r
- int index = Integer.parseInt(activeRes.get(i).toString());\r
+ int index = av.getColumnSelection().columnAt(i);\r
\r
if (anot[index] == null)\r
{\r
aa[activeRow].hasText = true;\r
}\r
\r
- for (int i = 0; i < activeRes.size(); i++)\r
+ for (int i = 0; i < av.getColumnSelection().size(); i++)\r
{\r
- int index = Integer.parseInt(activeRes.get(i).toString());\r
+ int index = av.getColumnSelection().columnAt(i);\r
\r
if (anot[index] == null)\r
{\r
}\r
\r
adjustPanelHeight();\r
- activeRes = null;\r
repaint();\r
\r
return;\r
*/\r
public void mousePressed(MouseEvent evt)\r
{\r
- int height = 0;\r
- activeRow = -1;\r
+\r
\r
AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
if(aa==null)\r
return;\r
\r
+\r
+ int height = 0;\r
+ activeRow = -1;\r
+\r
+\r
for (int i = 0; i < aa.length; i++)\r
{\r
if (aa[i].visible)\r
//Stretch Graph\r
graphStretch = i;\r
graphStretchY = evt.getY();\r
- activeRes = null;\r
- }\r
- else\r
- {\r
- activeRes = null;\r
}\r
\r
break;\r
}\r
}\r
\r
- if (SwingUtilities.isRightMouseButton(evt))\r
+\r
+ if (SwingUtilities.isRightMouseButton(evt) && activeRow!=-1)\r
{\r
- if (activeRes == null)\r
+ if (av.getColumnSelection() == null)\r
{\r
return;\r
}\r
\r
int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();\r
\r
- if (evt.isControlDown() || evt.isAltDown())\r
- {\r
- addEditableColumn(res);\r
- }\r
- else if (evt.isShiftDown())\r
+ min = res;\r
+ max = res;\r
+\r
+ if (av.getColumnSelection().contains(res))\r
+ av.getColumnSelection().removeElement(res);\r
+ else\r
{\r
- if (activeRes == null)\r
+ av.getColumnSelection().addElement(res);\r
+ SequenceGroup sg = new SequenceGroup();\r
+\r
+ for (int i = 0; i < av.alignment.getSequences().size(); i++)\r
{\r
- activeRes = new Vector();\r
+ sg.addSequence(av.alignment.getSequenceAt(i), false);\r
}\r
- else\r
- {\r
- int start = Integer.parseInt(activeRes.get(activeRes.size() -\r
- 1).toString());\r
- int end = res;\r
-\r
- if (end < start)\r
- {\r
- int temp = end;\r
- end = start;\r
- start = temp;\r
- }\r
\r
- for (int n = start; n <= end; n++)\r
- {\r
- addEditableColumn(n);\r
- }\r
- }\r
- }\r
- else\r
- {\r
- activeRes = new Vector();\r
- activeRes.addElement(String.valueOf(res));\r
+ sg.setStartRes(res);\r
+ sg.setEndRes(res);\r
+ av.setSelectionGroup(sg);\r
}\r
+\r
+ ap.repaint();\r
+\r
}\r
\r
/**\r
{\r
graphStretch = -1;\r
graphStretchY = -1;\r
+ mouseDragging = false;\r
}\r
\r
/**\r
*/\r
public void mouseEntered(MouseEvent evt)\r
{\r
+ if(mouseDragging)\r
+ ap.seqPanel.scrollCanvas(null);\r
}\r
\r
/**\r
*/\r
public void mouseExited(MouseEvent evt)\r
{\r
+ if(mouseDragging)\r
+ ap.seqPanel.scrollCanvas(evt);\r
}\r
\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
if(graphStretch>-1)\r
{\r
av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY - evt.getY();\r
- if(av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight <10)\r
- av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight = 10;\r
+ if(av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight <0)\r
+ av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight = 0;\r
graphStretchY = evt.getY();\r
adjustPanelHeight();\r
ap.repaint();\r
}\r
+ else\r
+ {\r
+ mouseDragging = true;\r
+\r
+ int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();\r
+\r
+ SequenceGroup sg = av.getSelectionGroup();\r
+\r
+ if (res < min)\r
+ {\r
+ min = res;\r
+ }\r
+\r
+ if (res > max)\r
+ {\r
+ max = res;\r
+ }\r
+\r
+ if (sg != null)\r
+ {\r
+ if (!av.getColumnSelection().contains(res))\r
+ {\r
+ av.getColumnSelection().addElement(res);\r
+ }\r
+\r
+ if (res > sg.getStartRes())\r
+ {\r
+ sg.setEndRes(res);\r
+ }\r
+ else if (res < sg.getStartRes())\r
+ {\r
+ sg.setStartRes(res);\r
+ }\r
+\r
+ for (int i = min; i <= max; i++)\r
+ {\r
+ if ((i < sg.getStartRes()) || (i > sg.getEndRes()))\r
+ {\r
+ av.getColumnSelection().removeElement(i);\r
+ }\r
+ else\r
+ {\r
+ av.getColumnSelection().addElement(i);\r
+ }\r
+ }\r
+\r
+ ap.repaint();\r
+ }\r
+\r
+ }\r
}\r
\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)\r
{\r
if(aa[row].graphGroup>-1)\r
\r
gg.setFont(av.getFont());\r
fm = gg.getFontMetrics();\r
+ gg.setColor(Color.white);\r
+ gg.fillRect(0, 0, imgWidth, image.getHeight());\r
}\r
\r
\r
*/\r
public void fastPaint(int horizontal)\r
{\r
- if ((horizontal == 0) || gg==null ||\r
- (av.alignment.getAlignmentAnnotation() == null) ||\r
- (av.alignment.getAlignmentAnnotation().length < 1))\r
+ if ((horizontal == 0)\r
+ || gg==null\r
+ || av.alignment.getAlignmentAnnotation()==null\r
+ || av.alignment.getAlignmentAnnotation().length < 1\r
+ || av.updatingConsensus\r
+ || av.updatingConservation)\r
{\r
repaint();\r
return;\r
*/\r
public void drawComponent(Graphics g, int startRes, int endRes)\r
{\r
- g.setFont(av.getFont());\r
+ if(av.updatingConsensus || av.updatingConservation)\r
+ {\r
+ //We'll keep a record of the old image,\r
+ //and draw a faded image until the calculation\r
+ //has completed\r
+ if(fadedImage==null\r
+ || fadedImage.getWidth()!=imgWidth\r
+ || fadedImage.getHeight()!=image.getHeight())\r
+ {\r
+ fadedImage = new BufferedImage(\r
+ imgWidth, image.getHeight(),\r
+ BufferedImage.TYPE_INT_RGB);\r
+\r
+ Graphics2D fadedG = (Graphics2D) fadedImage.getGraphics();\r
+\r
+ fadedG.setColor(Color.white);\r
+ fadedG.fillRect(0, 0, imgWidth, image.getHeight());\r
+\r
+ fadedG.setComposite(\r
+ AlphaComposite.getInstance(\r
+ AlphaComposite.SRC_OVER, .3f));\r
+ fadedG.drawImage(image, 0, 0, this);\r
\r
+ }\r
+\r
+ }\r
+ else\r
+ fadedImage = null;\r
+\r
+\r
+ g.setColor(Color.white);\r
+ g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight());\r
+\r
+ g.setFont(av.getFont());\r
if (fm == null)\r
fm = g.getFontMetrics();\r
\r
\r
- g.setColor(Color.white);\r
- g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight());\r
\r
- if ((av.alignment.getAlignmentAnnotation() == null) ||\r
+\r
+ if ( (av.alignment.getAlignmentAnnotation() == null) ||\r
(av.alignment.getAlignmentAnnotation().length < 1))\r
{\r
g.setColor(Color.white);\r
g.fillRect(0, 0, getWidth(), getHeight());\r
g.setColor(Color.black);\r
- g.drawString("Alignment has no annotations", 20, 15);\r
+ if(av.validCharWidth)\r
+ g.drawString("Alignment has no annotations", 20, 15);\r
\r
return;\r
}\r
\r
+\r
AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
\r
- int j;\r
- int x = 0;\r
- int y = 0;\r
- char[] lastSS = new char[aa.length];\r
- int[] lastSSX = new int[aa.length];\r
+ int x = 0, y = 0;\r
+ int column=0;\r
+ char lastSS;\r
+ int lastSSX;\r
int iconOffset = av.charHeight / 2;\r
boolean validRes = false;\r
\r
}\r
\r
\r
+ lastSS = ' ';\r
+ lastSSX = 0;\r
\r
if (row.graph>0)\r
{\r
}\r
}\r
\r
+ if (av.updatingConsensus && aa[i].label.equals("Consensus"))\r
+ {\r
+ y += av.charHeight;\r
+\r
+ g.drawImage(fadedImage,\r
+ 0,y-row.height,imgWidth, y,\r
+ 0,y-row.height,imgWidth, y, this);\r
+ g.setColor(Color.black);\r
+ // g.drawString("Calculating Consensus....",20, y-row.height/2);\r
+\r
+ continue;\r
+ }\r
+ else if (av.updatingConservation && aa[i].label.equals("Conservation"))\r
+ {\r
+\r
+ y += av.charHeight;\r
+ g.drawImage(fadedImage,\r
+ 0, y - row.height, imgWidth, y,\r
+ 0, y - row.height, imgWidth, y, this);\r
+\r
+ g.setColor(Color.black);\r
+ // g.drawString("Calculating Conservation.....",20, y-row.height/2);\r
+\r
+ continue;\r
+ }\r
+ else if (av.updatingConservation && aa[i].label.equals("Quality"))\r
+ {\r
+\r
+ y += av.charHeight;\r
+ g.drawImage(fadedImage,\r
+ 0, y - row.height, imgWidth, y,\r
+ 0, y - row.height, imgWidth, y, this);\r
+ g.setColor(Color.black);\r
+ /// g.drawString("Calculating Quality....",20, y-row.height/2);\r
+\r
+ continue;\r
+ }\r
+\r
+\r
if (row.hasText)\r
{\r
- iconOffset = av.charHeight / 2;\r
+ iconOffset = av.charHeight / 2 + 4;\r
}\r
else\r
{\r
iconOffset = 0;\r
}\r
\r
- for (j = startRes; j < endRes; j++)\r
+ x = 0;\r
+ while (x < endRes-startRes)\r
{\r
- if ((row.annotations.length <= j) ||\r
- (row.annotations[j] == null))\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
+\r
+ if ((row.annotations.length <= column) ||\r
+ (row.annotations[column] == null))\r
{\r
validRes = false;\r
}\r
validRes = true;\r
}\r
\r
- x = (j - startRes) * av.charWidth;\r
\r
if (activeRow == i)\r
{\r
g.setColor(Color.red);\r
\r
- if (activeRes != null)\r
+ if (av.getColumnSelection() != null)\r
{\r
- for (int n = 0; n < activeRes.size(); n++)\r
+ for (int n = 0; n < av.getColumnSelection().size(); n++)\r
{\r
- int v = Integer.parseInt(activeRes.get(n).toString());\r
+ int v = av.getColumnSelection().columnAt(n);\r
\r
- if (v == j)\r
+ if (v == column)\r
{\r
- g.fillRect((j - startRes) * av.charWidth, y,\r
- av.charWidth, row.height);\r
+ g.fillRect(x * av.charWidth, y,\r
+ av.charWidth, av.charHeight);\r
}\r
}\r
}\r
}\r
\r
- if (validRes &&\r
- (row.annotations[j].displayCharacter.length() > 0))\r
+ if (av.validCharWidth && validRes &&\r
+ (row.annotations[column].displayCharacter.length() > 0))\r
{\r
\r
int charOffset = (av.charWidth -\r
- fm.charWidth(row.annotations[j].displayCharacter.charAt(\r
+ fm.charWidth(row.annotations[column].displayCharacter.charAt(\r
0))) / 2;\r
- g.setColor(row.annotations[j].colour);\r
+ g.setColor(row.annotations[column].colour);\r
\r
- if (j == 0 || row.graph>0)\r
+ if (column == 0 || row.graph>0)\r
{\r
- g.drawString(row.annotations[j].displayCharacter, x+charOffset,\r
- y + iconOffset + 3);\r
+ g.drawString(row.annotations[column].displayCharacter,\r
+ (x*av.charWidth)+charOffset,\r
+ y + iconOffset );\r
}\r
- else if (((row.annotations[j - 1] == null) ||\r
- (row.annotations[j].displayCharacter != row.annotations[j -\r
- 1].displayCharacter)))\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[j].displayCharacter, x+charOffset,\r
- y + iconOffset + 3);\r
+ g.drawString(row.annotations[column].displayCharacter,\r
+ x*av.charWidth+charOffset,\r
+ y + iconOffset );\r
}\r
}\r
\r
if (row.hasIcons)\r
{\r
if (!validRes ||\r
- (row.annotations[j].secondaryStructure != lastSS[i]))\r
+ (row.annotations[column].secondaryStructure != lastSS))\r
{\r
- switch (lastSS[i])\r
+ switch (lastSS)\r
{\r
case 'H':\r
- g.setColor(HELIX_COLOUR);\r
- g.fillRoundRect(lastSSX[i], y + 4 + iconOffset,\r
- x - lastSSX[i], 7, 8, 8);\r
-\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[i], y + 4 + iconOffset,\r
- x - lastSSX[i] - 4, 7);\r
- g.fillPolygon(new int[] { x - 4, x - 4, x },\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
\r
default:\r
g.setColor(Color.gray);\r
- g.fillRect(lastSSX[i], y + 6 + iconOffset,\r
- x - lastSSX[i], 2);\r
+ g.fillRect(lastSSX, y + 6 + iconOffset,\r
+ (x*av.charWidth) - lastSSX, 2);\r
\r
break;\r
}\r
\r
if (validRes)\r
{\r
- lastSS[i] = row.annotations[j].secondaryStructure;\r
+ lastSS = row.annotations[column].secondaryStructure;\r
}\r
else\r
{\r
- lastSS[i] = ' ';\r
+ lastSS = ' ';\r
}\r
\r
- lastSSX[i] = x;\r
+ lastSSX = (x*av.charWidth);\r
}\r
}\r
+\r
+\r
+ column++;\r
+ x++;\r
}\r
\r
- x += av.charWidth;\r
+ if(column>=row.annotations.length)\r
+ column = row.annotations.length-1;\r
+\r
+ // x ++;\r
\r
if (row.hasIcons)\r
{\r
- switch (lastSS[i])\r
- {\r
+ switch (lastSS)\r
+ {\r
case 'H':\r
- g.setColor(HELIX_COLOUR);\r
- g.fillRoundRect(lastSSX[i], y + 4 + iconOffset,\r
- x - lastSSX[i], 7, 8, 8);\r
-\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
- case 'E':\r
- g.setColor(SHEET_COLOUR);\r
+ int sCol = (lastSSX / av.charWidth) + startRes;\r
+ int x1 = lastSSX;\r
+ int x2 = (x*av.charWidth);\r
\r
- if (row.annotations[endRes] !=null\r
- && row.annotations[endRes].secondaryStructure != 'E')\r
- {\r
- g.fillRect(lastSSX[i], y + 4 + iconOffset,\r
- x - lastSSX[i] - 4, 7);\r
- g.fillPolygon(new int[]\r
- {x - 4, x - 4, x},\r
- new int[]\r
- {\r
- y + iconOffset, y + 14 + iconOffset,\r
- y + 7 + iconOffset\r
- }, 3);\r
- }\r
- else\r
- g.fillRect(lastSSX[i], y + 4 + iconOffset,\r
- x - lastSSX[i], 7);\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
- break;\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
- case 'C':\r
- break;\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+1) * av.charWidth - lastSSX, 7);\r
+ }\r
+ break;\r
\r
default:\r
- g.setColor(Color.gray);\r
- g.fillRect(lastSSX[i], y + 6 + iconOffset, x - lastSSX[i], 2);\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
+ break;\r
+ }\r
+ }\r
\r
- if (row.graph>0)\r
+ if (row.graph>0 && row.graphHeight>0)\r
{\r
if(row.graph == AlignmentAnnotation.LINE_GRAPH )\r
{\r
if(sRes>aa.annotations.length)\r
return;\r
\r
+\r
int x = 0;\r
\r
//Adjustment for fastpaint to left\r
if(eRes<av.endRes)\r
eRes++;\r
\r
+ eRes = Math.min(eRes, aa.annotations.length);\r
+\r
if(sRes==0)\r
{\r
- sRes++;\r
- x+=av.charWidth;\r
+ x++;\r
}\r
\r
int y1=y, y2=y;\r
\r
////Draw origin\r
if(min<0)\r
- y2 = (int)(y - (0-min / range)*graphHeight);\r
+ y2 = y - (int)((0-min / range)*graphHeight);\r
\r
g.setColor(Color.gray);\r
g.drawLine(x-av.charWidth,y2,(eRes-sRes+1)*av.charWidth,y2);\r
\r
+ eRes = Math.min(eRes, aa.annotations.length);\r
+\r
+ int column;\r
+ int aaMax = aa.annotations.length-1;\r
\r
- if(aa.threshold!=null)\r
+ while( x < eRes - sRes )\r
{\r
- g.setColor(aa.threshold.colour);\r
- Graphics2D g2 = (Graphics2D)g;\r
- g2.setStroke(new BasicStroke(1,\r
- BasicStroke.CAP_SQUARE,\r
- BasicStroke.JOIN_ROUND, 3f,\r
- new float[] { 5f, 3f }, 0f));\r
+ column = sRes + x;\r
+ if(av.hasHiddenColumns)\r
+ {\r
+ column = av.getColumnSelection().adjustForHiddenColumns(column);\r
+ }\r
\r
- y2 = (int)(y - ((aa.threshold.value-min) / range)*graphHeight);\r
- g.drawLine(x-av.charWidth,y2,(eRes-sRes+1)*av.charWidth,y2);\r
- g2.setStroke(new BasicStroke());\r
- }\r
+ if (column > aaMax)\r
+ {\r
+ break;\r
+ }\r
\r
- eRes = Math.min(eRes, aa.annotations.length);\r
- for (int j = sRes; j < eRes; j++)\r
- {\r
- if(aa.annotations[j]==null || aa.annotations[j-1]==null)\r
+ if(aa.annotations[column]==null || aa.annotations[column-1]==null)\r
{\r
- x+=av.charWidth;\r
+ x++;\r
continue;\r
}\r
- g.setColor(aa.annotations[j].colour);\r
- y1 = y - (int) (((aa.annotations[j-1].value-min) / range) * graphHeight);\r
- y2 = y - (int) (((aa.annotations[j].value-min) / range) * graphHeight);\r
- g.drawLine(x-av.charWidth/2, y1, x+av.charWidth/2, y2);\r
- x += av.charWidth;\r
+\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.drawLine(x*av.charWidth-av.charWidth/2, y1, x*av.charWidth+av.charWidth/2, y2);\r
+ x ++;\r
}\r
+\r
+ if(aa.threshold!=null)\r
+ {\r
+ g.setColor(aa.threshold.colour);\r
+ Graphics2D g2 = (Graphics2D)g;\r
+ g2.setStroke(new BasicStroke(1,\r
+ BasicStroke.CAP_SQUARE,\r
+ BasicStroke.JOIN_ROUND, 3f,\r
+ new float[] { 5f, 3f }, 0f));\r
+\r
+ y2 = (int)(y - ((aa.threshold.value-min) / range)*graphHeight);\r
+ g.drawLine(0,y2,(eRes-sRes)*av.charWidth,y2);\r
+ g2.setStroke(new BasicStroke());\r
+ }\r
}\r
\r
public void drawBarGraph(Graphics g, AlignmentAnnotation aa,\r
if(sRes>aa.annotations.length)\r
return;\r
\r
- int x=0, y1, y2;\r
-\r
- float range = max - min;\r
-\r
- if(aa.threshold!=null)\r
- {\r
- g.setColor(aa.threshold.colour);\r
- Graphics2D g2 = (Graphics2D)g;\r
- g2.setStroke(new BasicStroke(1,\r
- BasicStroke.CAP_SQUARE,\r
- BasicStroke.JOIN_ROUND, 3f,\r
- new float[] { 5f, 3f }, 0f));\r
+ eRes = Math.min(eRes, aa.annotations.length);\r
\r
- y2 = (int)(y - ((aa.threshold.value-min) / range)*aa.graphHeight);\r
- g.drawLine(x-av.charWidth,y2,(eRes-sRes+1)*av.charWidth,y2);\r
- g2.setStroke(new BasicStroke());\r
- }\r
+ int x=0, y1=y, y2=y;\r
\r
- y1 = y2 = y;\r
+ float range = max - min;\r
\r
if(min<0)\r
- y2 = (int)(y - (0-min / (range))*aa.graphHeight);\r
+ y2 = y - (int)((0-min / (range))*aa.graphHeight);\r
\r
g.setColor(Color.gray);\r
\r
- g.drawLine(x,y2,(eRes-sRes+1)*av.charWidth,y2);\r
-\r
- eRes = Math.min(eRes, aa.annotations.length-1);\r
+ g.drawLine(x,y2,(eRes-sRes)*av.charWidth,y2);\r
\r
+ int column;\r
+ int aaMax = aa.annotations.length-1;\r
\r
- for (int j = sRes; j < eRes; j++)\r
+ while( x < eRes-sRes )\r
{\r
+ column = sRes + x;\r
+ if(av.hasHiddenColumns)\r
+ {\r
+ column = av.getColumnSelection().adjustForHiddenColumns(column);\r
+ }\r
\r
- if (aa.annotations[j] == null)\r
+ if(column > aaMax)\r
{\r
- x += av.charWidth;\r
+ break;\r
+ }\r
+\r
+ if (aa.annotations[column] == null)\r
+ {\r
+ x ++;\r
continue;\r
}\r
\r
- g.setColor(aa.annotations[j].colour);\r
- y1 = y - (int) (((aa.annotations[j].value-min) / (range)) * aa.graphHeight);\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, y2, av.charWidth, y1-y2 );\r
+ g.fillRect(x*av.charWidth, y2, av.charWidth, y1-y2 );\r
else\r
- g.fillRect(x, y1, av.charWidth, y2-y1 );\r
+ g.fillRect(x*av.charWidth, y1, av.charWidth, y2-y1 );\r
+\r
+ x ++ ;\r
\r
- x += av.charWidth;\r
}\r
+ if(aa.threshold!=null)\r
+ {\r
+ g.setColor(aa.threshold.colour);\r
+ Graphics2D g2 = (Graphics2D)g;\r
+ g2.setStroke(new BasicStroke(1,\r
+ BasicStroke.CAP_SQUARE,\r
+ BasicStroke.JOIN_ROUND, 3f,\r
+ new float[] { 5f, 3f }, 0f));\r
\r
+ y2 = (int)(y - ((aa.threshold.value-min) / range)*aa.graphHeight);\r
+ g.drawLine(0,y2,(eRes-sRes)*av.charWidth,y2);\r
+ g2.setStroke(new BasicStroke());\r
+ }\r
}\r
\r
// used by overview window\r
public void drawGraph(Graphics g, AlignmentAnnotation aa, int width, int y, int sRes, int eRes)\r
{\r
+ eRes = Math.min(eRes, aa.annotations.length);\r
g.setColor(Color.white);\r
g.fillRect(0, 0, width, y);\r
g.setColor(new Color(0, 0, 180));\r
\r
for (int j = sRes; j < eRes; j++)\r
{\r
+ if (aa.annotations[j] != null)\r
+ {\r
g.setColor(aa.annotations[j].colour);\r
\r
- height = (int) ((aa.annotations[j].value / aa.graphMax) * y);\r
- if(height>y)\r
+ height = (int) ( (aa.annotations[j].value / aa.graphMax) * y);\r
+ if (height > y)\r
height = y;\r
\r
g.fillRect(x, y - height, av.charWidth, height);\r
+ }\r
x += av.charWidth;\r
}\r
}\r
git://source.jalview.org / jalview.git / blobdiff