/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2007 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
*/\r
package jalview.gui;\r
\r
-import jalview.datamodel.*;\r
-\r
import java.awt.*;\r
import java.awt.event.*;\r
import java.awt.image.*;\r
-\r
import javax.swing.*;\r
\r
+import jalview.datamodel.*;\r
\r
/**\r
* DOCUMENT ME!\r
* @author $author$\r
* @version $Revision$\r
*/\r
-public class AnnotationPanel extends JPanel implements MouseListener,\r
+public class AnnotationPanel\r
+ extends JPanel implements MouseListener,\r
MouseMotionListener, ActionListener, AdjustmentListener\r
{\r
- final String HELIX = "Helix";\r
- final String SHEET = "Sheet";\r
- final String LABEL = "Label";\r
- final String REMOVE = "Remove Annotation";\r
- final String COLOUR = "Colour";\r
- final Color HELIX_COLOUR = Color.red.darker();\r
- final Color SHEET_COLOUR = Color.green.darker().darker();\r
-\r
- /** DOCUMENT ME!! */\r
- AlignViewport av;\r
- AlignmentPanel ap;\r
- int activeRow = -1;\r
- BufferedImage image;\r
- BufferedImage fadedImage;\r
- Graphics2D gg;\r
- FontMetrics fm;\r
- int imgWidth = 0;\r
- boolean fastPaint = false;\r
-\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
- * @param ap DOCUMENT ME!\r
- */\r
- public AnnotationPanel(AlignmentPanel ap)\r
+ final String HELIX = "Helix";\r
+ final String SHEET = "Sheet";\r
+ final String LABEL = "Label";\r
+ final String REMOVE = "Remove Annotation";\r
+ final String COLOUR = "Colour";\r
+ final Color HELIX_COLOUR = Color.red.darker();\r
+ final Color SHEET_COLOUR = Color.green.darker().darker();\r
+\r
+ /** DOCUMENT ME!! */\r
+ AlignViewport av;\r
+ AlignmentPanel ap;\r
+ int activeRow = -1;\r
+ BufferedImage image;\r
+ BufferedImage fadedImage;\r
+ Graphics2D gg;\r
+ FontMetrics fm;\r
+ int imgWidth = 0;\r
+ boolean fastPaint = false;\r
+\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
+ * @param ap DOCUMENT ME!\r
+ */\r
+ public AnnotationPanel(AlignmentPanel ap)\r
+ {\r
+\r
+ if (System.getProperty("os.name").startsWith("Mac"))\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
- this.ap = ap;\r
- av = ap.av;\r
- this.setLayout(null);\r
- addMouseListener(this);\r
- addMouseMotionListener(this);\r
- 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
- * @param evt DOCUMENT ME!\r
- */\r
- public void adjustmentValueChanged(AdjustmentEvent evt)\r
- {\r
- ap.alabels.setScrollOffset(-evt.getValue());\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- */\r
- public int adjustPanelHeight()\r
+ ToolTipManager.sharedInstance().registerComponent(this);\r
+ ToolTipManager.sharedInstance().setInitialDelay(0);\r
+ ToolTipManager.sharedInstance().setDismissDelay(10000);\r
+ this.ap = ap;\r
+ av = ap.av;\r
+ this.setLayout(null);\r
+ addMouseListener(this);\r
+ addMouseMotionListener(this);\r
+ ap.annotationScroller.getVerticalScrollBar().addAdjustmentListener(this);\r
+ }\r
+\r
+ public AnnotationPanel(AlignViewport av)\r
+ {\r
+ this.av = av;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
+ public void adjustmentValueChanged(AdjustmentEvent evt)\r
+ {\r
+ ap.alabels.setScrollOffset( -evt.getValue());\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
+ public int adjustPanelHeight()\r
+ {\r
+ // setHeight of panels\r
+ AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
+ int height = 0;\r
+\r
+ if (aa != null)\r
{\r
- // setHeight of panels\r
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
- int height = 0;\r
-\r
- if (aa != null)\r
+ for (int i = 0; i < aa.length; i++)\r
+ {\r
+ if (!aa[i].visible)\r
{\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
-\r
- if (aa[i].hasText)\r
- {\r
- aa[i].height += av.charHeight;\r
- }\r
-\r
- if (aa[i].hasIcons)\r
- {\r
- aa[i].height += 16;\r
- }\r
+ continue;\r
+ }\r
\r
- if (aa[i].graph>0)\r
- {\r
- aa[i].height += aa[i].graphHeight;\r
- }\r
+ aa[i].height = 0;\r
\r
- if (aa[i].height == 0)\r
- {\r
- aa[i].height = 20;\r
- }\r
+ if (aa[i].hasText)\r
+ {\r
+ aa[i].height += av.charHeight;\r
+ }\r
\r
- height += aa[i].height;\r
- }\r
+ if (aa[i].hasIcons)\r
+ {\r
+ aa[i].height += 16;\r
}\r
- else\r
+\r
+ if (aa[i].graph > 0)\r
{\r
- height = 20;\r
+ aa[i].height += aa[i].graphHeight;\r
}\r
\r
- this.setPreferredSize(new Dimension(1, height));\r
+ if (aa[i].height == 0)\r
+ {\r
+ aa[i].height = 20;\r
+ }\r
\r
- return height;\r
+ height += aa[i].height;\r
+ }\r
}\r
-\r
-\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\r
- */\r
- public void actionPerformed(ActionEvent evt)\r
+ else\r
{\r
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
- Annotation[] anot = aa[activeRow].annotations;\r
+ height = 20;\r
+ }\r
\r
- if (anot.length < av.getColumnSelection().getMax())\r
- {\r
- Annotation[] temp = new Annotation[av.getColumnSelection().getMax()+2 ];\r
- System.arraycopy(anot, 0, temp, 0, anot.length);\r
- anot = temp;\r
- aa[activeRow].annotations = anot;\r
- }\r
+ this.setPreferredSize(new Dimension(1, height));\r
\r
+ return height;\r
+ }\r
\r
- if (evt.getActionCommand().equals(REMOVE))\r
- {\r
- for (int i = 0; i < av.getColumnSelection().size(); i++)\r
- {\r
- anot[av.getColumnSelection().columnAt(i)] = null;\r
- }\r
- }\r
- else if (evt.getActionCommand().equals(LABEL))\r
- {\r
- String label = JOptionPane.showInputDialog(this, "Enter Label ",\r
- "Enter label", JOptionPane.QUESTION_MESSAGE);\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
+ public void actionPerformed(ActionEvent evt)\r
+ {\r
+ AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
+ Annotation[] anot = aa[activeRow].annotations;\r
\r
- if (label == null)\r
- {\r
- return;\r
- }\r
+ if (anot.length < av.getColumnSelection().getMax())\r
+ {\r
+ Annotation[] temp = new Annotation[av.getColumnSelection().getMax() + 2];\r
+ System.arraycopy(anot, 0, temp, 0, anot.length);\r
+ anot = temp;\r
+ aa[activeRow].annotations = anot;\r
+ }\r
\r
- if ((label.length() > 0) && !aa[activeRow].hasText)\r
- {\r
- aa[activeRow].hasText = true;\r
- }\r
+ if (evt.getActionCommand().equals(REMOVE))\r
+ {\r
+ for (int i = 0; i < av.getColumnSelection().size(); i++)\r
+ {\r
+ anot[av.getColumnSelection().columnAt(i)] = null;\r
+ }\r
+ }\r
+ else if (evt.getActionCommand().equals(LABEL))\r
+ {\r
+ String label = JOptionPane.showInputDialog(this, "Enter Label ",\r
+ "Enter label",\r
+ JOptionPane.QUESTION_MESSAGE);\r
\r
- for (int i = 0; i < av.getColumnSelection().size(); i++)\r
- {\r
- int index = av.getColumnSelection().columnAt(i);\r
+ if (label == null)\r
+ {\r
+ return;\r
+ }\r
\r
- if (anot[index] == null)\r
- {\r
- anot[index] = new Annotation(label, "", ' ', 0);\r
- }\r
+ if ( (label.length() > 0) && !aa[activeRow].hasText)\r
+ {\r
+ aa[activeRow].hasText = true;\r
+ }\r
\r
- anot[index].displayCharacter = label;\r
- }\r
- }\r
- else if (evt.getActionCommand().equals(COLOUR))\r
+ for (int i = 0; i < av.getColumnSelection().size(); i++)\r
+ {\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
+ anot[index] = new Annotation(label, "", ' ', 0);\r
+ }\r
\r
- for (int i = 0; i < av.getColumnSelection().size(); i++)\r
- {\r
- int index = av.getColumnSelection().columnAt(i);\r
+ anot[index].displayCharacter = label;\r
+ }\r
+ }\r
+ else if (evt.getActionCommand().equals(COLOUR))\r
+ {\r
+ Color col = JColorChooser.showDialog(this,\r
+ "Choose foreground colour",\r
+ Color.black);\r
\r
- if (anot[index] == null)\r
- {\r
- anot[index] = new Annotation("", "", ' ', 0);\r
- }\r
+ for (int i = 0; i < av.getColumnSelection().size(); i++)\r
+ {\r
+ int index = av.getColumnSelection().columnAt(i);\r
\r
- anot[index].colour = col;\r
- }\r
- }\r
- else // HELIX OR SHEET\r
+ if (anot[index] == null)\r
{\r
- char type = 0;\r
- String symbol = "\u03B1";\r
+ anot[index] = new Annotation("", "", ' ', 0);\r
+ }\r
\r
- if (evt.getActionCommand().equals(HELIX))\r
- {\r
- type = 'H';\r
- }\r
- else if (evt.getActionCommand().equals(SHEET))\r
- {\r
- type = 'E';\r
- symbol = "\u03B2";\r
- }\r
+ anot[index].colour = col;\r
+ }\r
+ }\r
+ else // HELIX OR SHEET\r
+ {\r
+ char type = 0;\r
+ String symbol = "\u03B1";\r
\r
- if (!aa[activeRow].hasIcons)\r
- {\r
- aa[activeRow].hasIcons = true;\r
- }\r
+ if (evt.getActionCommand().equals(HELIX))\r
+ {\r
+ type = 'H';\r
+ }\r
+ else if (evt.getActionCommand().equals(SHEET))\r
+ {\r
+ type = 'E';\r
+ symbol = "\u03B2";\r
+ }\r
\r
- String label = JOptionPane.showInputDialog("Enter a label for the structure?",\r
- symbol);\r
+ if (!aa[activeRow].hasIcons)\r
+ {\r
+ aa[activeRow].hasIcons = true;\r
+ }\r
\r
- if (label == null)\r
- {\r
- return;\r
- }\r
+ String label = JOptionPane.showInputDialog(\r
+ "Enter a label for the structure?",\r
+ symbol);\r
\r
- if ((label.length() > 0) && !aa[activeRow].hasText)\r
- {\r
- aa[activeRow].hasText = true;\r
- }\r
+ if (label == null)\r
+ {\r
+ return;\r
+ }\r
\r
- for (int i = 0; i < av.getColumnSelection().size(); i++)\r
- {\r
- int index = av.getColumnSelection().columnAt(i);\r
+ if ( (label.length() > 0) && !aa[activeRow].hasText)\r
+ {\r
+ aa[activeRow].hasText = true;\r
+ }\r
\r
- if (anot[index] == null)\r
- {\r
- anot[index] = new Annotation(label, "", type, 0);\r
- }\r
+ for (int i = 0; i < av.getColumnSelection().size(); i++)\r
+ {\r
+ int index = av.getColumnSelection().columnAt(i);\r
\r
- anot[index].secondaryStructure = type;\r
- anot[index].displayCharacter = label;\r
- }\r
+ if (anot[index] == null)\r
+ {\r
+ anot[index] = new Annotation(label, "", type, 0);\r
}\r
\r
- adjustPanelHeight();\r
- repaint();\r
-\r
- return;\r
+ anot[index].secondaryStructure = type;\r
+ anot[index].displayCharacter = label;\r
+ }\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\r
- */\r
- public void mousePressed(MouseEvent evt)\r
- {\r
-\r
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
- if(aa==null)\r
- return;\r
+ adjustPanelHeight();\r
+ repaint();\r
\r
+ return;\r
+ }\r
\r
- int height = 0;\r
- activeRow = -1;\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
+ public void mousePressed(MouseEvent evt)\r
+ {\r
\r
+ AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
+ if (aa == null)\r
+ {\r
+ return;\r
+ }\r
\r
- for (int i = 0; i < aa.length; i++)\r
- {\r
- if (aa[i].visible)\r
- {\r
- height += aa[i].height;\r
- }\r
-\r
- if (evt.getY() < height)\r
- {\r
- if (aa[i].editable)\r
- {\r
- activeRow = i;\r
- }\r
- else if(aa[i].graph>0)\r
- {\r
- //Stretch Graph\r
- graphStretch = i;\r
- graphStretchY = evt.getY();\r
- }\r
-\r
- break;\r
- }\r
- }\r
+ int height = 0;\r
+ activeRow = -1;\r
\r
+ for (int i = 0; i < aa.length; i++)\r
+ {\r
+ if (aa[i].visible)\r
+ {\r
+ height += aa[i].height;\r
+ }\r
\r
- if (SwingUtilities.isRightMouseButton(evt) && activeRow!=-1)\r
+ if (evt.getY() < height)\r
+ {\r
+ if (aa[i].editable)\r
{\r
- if (av.getColumnSelection() == null)\r
- {\r
- return;\r
- }\r
-\r
- JPopupMenu pop = new JPopupMenu("Structure type");\r
- JMenuItem item = new JMenuItem(HELIX);\r
- item.addActionListener(this);\r
- pop.add(item);\r
- item = new JMenuItem(SHEET);\r
- item.addActionListener(this);\r
- pop.add(item);\r
- item = new JMenuItem(LABEL);\r
- item.addActionListener(this);\r
- pop.add(item);\r
- item = new JMenuItem(COLOUR);\r
- item.addActionListener(this);\r
- pop.add(item);\r
- item = new JMenuItem(REMOVE);\r
- item.addActionListener(this);\r
- pop.add(item);\r
- pop.show(this, evt.getX(), evt.getY());\r
-\r
- return;\r
+ activeRow = i;\r
}\r
-\r
- if (aa == null)\r
+ else if (aa[i].graph > 0)\r
{\r
- return;\r
+ //Stretch Graph\r
+ graphStretch = i;\r
+ graphStretchY = evt.getY();\r
}\r
\r
- int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();\r
+ break;\r
+ }\r
+ }\r
\r
- if(av.hasHiddenColumns)\r
- res = av.getColumnSelection().adjustForHiddenColumns(res);\r
+ if (SwingUtilities.isRightMouseButton(evt) && activeRow != -1)\r
+ {\r
+ if (av.getColumnSelection() == null)\r
+ {\r
+ return;\r
+ }\r
\r
- min = res;\r
- max = res;\r
+ JPopupMenu pop = new JPopupMenu("Structure type");\r
+ JMenuItem item = new JMenuItem(HELIX);\r
+ item.addActionListener(this);\r
+ pop.add(item);\r
+ item = new JMenuItem(SHEET);\r
+ item.addActionListener(this);\r
+ pop.add(item);\r
+ item = new JMenuItem(LABEL);\r
+ item.addActionListener(this);\r
+ pop.add(item);\r
+ item = new JMenuItem(COLOUR);\r
+ item.addActionListener(this);\r
+ pop.add(item);\r
+ item = new JMenuItem(REMOVE);\r
+ item.addActionListener(this);\r
+ pop.add(item);\r
+ pop.show(this, evt.getX(), evt.getY());\r
+\r
+ return;\r
+ }\r
\r
- if (av.getColumnSelection().contains(res))\r
- av.getColumnSelection().removeElement(res);\r
- else\r
- {\r
- av.getColumnSelection().addElement(res);\r
- SequenceGroup sg = new SequenceGroup();\r
+ if (aa == null)\r
+ {\r
+ return;\r
+ }\r
\r
- for (int i = 0; i < av.alignment.getSequences().size(); i++)\r
- {\r
- sg.addSequence(av.alignment.getSequenceAt(i), false);\r
- }\r
+ int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();\r
\r
- sg.setStartRes(res);\r
- sg.setEndRes(res);\r
- av.setSelectionGroup(sg);\r
- }\r
+ if (av.hasHiddenColumns)\r
+ {\r
+ res = av.getColumnSelection().adjustForHiddenColumns(res);\r
+ }\r
\r
- ap.repaint();\r
+ min = res;\r
+ max = res;\r
\r
+ if (av.getColumnSelection().contains(res))\r
+ {\r
+ av.getColumnSelection().removeElement(res);\r
}\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\r
- */\r
- public void mouseReleased(MouseEvent evt)\r
+ else\r
{\r
- graphStretch = -1;\r
- graphStretchY = -1;\r
- mouseDragging = false;\r
+ av.getColumnSelection().addElement(res);\r
+ SequenceGroup sg = new SequenceGroup();\r
+\r
+ for (int i = 0; i < av.alignment.getSequences().size(); i++)\r
+ {\r
+ sg.addSequence(av.alignment.getSequenceAt(i), false);\r
+ }\r
+\r
+ sg.setStartRes(res);\r
+ sg.setEndRes(res);\r
+ av.setSelectionGroup(sg);\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\r
- */\r
- public void mouseEntered(MouseEvent evt)\r
+ ap.repaint();\r
+\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
+ public void mouseReleased(MouseEvent evt)\r
+ {\r
+ graphStretch = -1;\r
+ graphStretchY = -1;\r
+ mouseDragging = false;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
+ public void mouseEntered(MouseEvent evt)\r
+ {\r
+ if (mouseDragging)\r
{\r
- if(mouseDragging)\r
- ap.seqPanel.scrollCanvas(null);\r
+ ap.seqPanel.scrollCanvas(null);\r
}\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\r
- */\r
- public void mouseExited(MouseEvent evt)\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
+ public void mouseExited(MouseEvent evt)\r
+ {\r
+ if (mouseDragging)\r
{\r
- if(mouseDragging)\r
- ap.seqPanel.scrollCanvas(evt);\r
+ ap.seqPanel.scrollCanvas(evt);\r
}\r
-\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\r
- */\r
- public void mouseDragged(MouseEvent evt)\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
+ public void mouseDragged(MouseEvent evt)\r
+ {\r
+ if (graphStretch > -1)\r
{\r
- if(graphStretch>-1)\r
+ av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight +=\r
+ graphStretchY - evt.getY();\r
+ if (av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight < 0)\r
{\r
- av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY - evt.getY();\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
+ av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight = 0;\r
}\r
- else\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
+ if (av.hasHiddenColumns)\r
{\r
- mouseDragging = true;\r
+ res = av.getColumnSelection().adjustForHiddenColumns(res);\r
+ }\r
\r
- int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();\r
+ SequenceGroup sg = av.getSelectionGroup();\r
\r
- if(av.hasHiddenColumns)\r
- res = av.getColumnSelection().adjustForHiddenColumns(res);\r
+ if (res < min)\r
+ {\r
+ min = res;\r
+ }\r
\r
- SequenceGroup sg = av.getSelectionGroup();\r
+ if (res > max)\r
+ {\r
+ max = res;\r
+ }\r
\r
- if (res < min)\r
+ if (sg != null)\r
+ {\r
+ if (!av.getColumnSelection().contains(res))\r
{\r
- min = res;\r
+ av.getColumnSelection().addElement(res);\r
}\r
\r
- if (res > max)\r
+ if (res > sg.getStartRes())\r
{\r
- max = res;\r
+ sg.setEndRes(res);\r
}\r
-\r
- if (sg != null)\r
+ else if (res < sg.getStartRes())\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
+ sg.setStartRes(res);\r
+ }\r
\r
- ap.repaint();\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
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\r
- */\r
- public void mouseMoved(MouseEvent evt)\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
+ public void mouseMoved(MouseEvent evt)\r
+ {\r
+ AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
+\r
+ if (aa == null)\r
{\r
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
-\r
- if (aa == null)\r
- {\r
- this.setToolTipText(null);\r
- return;\r
- }\r
+ this.setToolTipText(null);\r
+ return;\r
+ }\r
\r
- int row = -1;\r
- int height = 0;\r
+ int row = -1;\r
+ int height = 0;\r
\r
- for (int i = 0; i < aa.length; i++)\r
- {\r
- if (aa[i].visible)\r
- {\r
- height += aa[i].height;\r
- }\r
+ for (int i = 0; i < aa.length; i++)\r
+ {\r
+ if (aa[i].visible)\r
+ {\r
+ height += aa[i].height;\r
+ }\r
\r
- if (evt.getY() < height)\r
- {\r
- row = i;\r
+ if (evt.getY() < height)\r
+ {\r
+ row = i;\r
\r
- break;\r
- }\r
- }\r
+ break;\r
+ }\r
+ }\r
\r
- if(row==-1)\r
- {\r
- this.setToolTipText(null);\r
- return;\r
- }\r
+ if (row == -1)\r
+ {\r
+ this.setToolTipText(null);\r
+ return;\r
+ }\r
\r
- int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();\r
+ int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();\r
\r
- if(av.hasHiddenColumns)\r
- res = av.getColumnSelection().adjustForHiddenColumns(res);\r
+ if (av.hasHiddenColumns)\r
+ {\r
+ res = av.getColumnSelection().adjustForHiddenColumns(res);\r
+ }\r
\r
- if ( aa[row].annotations!=null\r
- && row > -1\r
- && res < (int) aa[row].annotations.length)\r
+ if (aa[row].annotations != null\r
+ && row > -1\r
+ && res < (int) aa[row].annotations.length)\r
+ {\r
+ if (aa[row].graphGroup > -1)\r
+ {\r
+ StringBuffer tip = new StringBuffer("<html>");\r
+ for (int gg = 0; gg < aa.length; gg++)\r
{\r
- if(aa[row].graphGroup>-1)\r
- {\r
- StringBuffer tip = new StringBuffer("<html>");\r
- for (int gg = 0; gg < aa.length; gg++)\r
- {\r
- if (aa[gg].graphGroup == aa[row].graphGroup && aa[gg].annotations[res]!=null)\r
- tip.append(aa[gg].label+" "+aa[gg].annotations[res].description+"<br>" );\r
- }\r
- if(tip.length()!=6)\r
- {\r
- tip.setLength(tip.length() - 4);\r
- this.setToolTipText(tip.toString() + "</html>");\r
- }\r
- }\r
- else if(aa[row].annotations[res] != null\r
- && aa[row].annotations[res].description!=null)\r
- this.setToolTipText(aa[row].annotations[res].description);\r
-\r
- if(aa[row].annotations[res]!=null)\r
- {\r
- StringBuffer text = new StringBuffer("Sequence position " +\r
- (res + 1));\r
+ if (aa[gg].graphGroup == aa[row].graphGroup && aa[gg].annotations[res] != null)\r
+ {\r
+ tip.append(aa[gg].label + " " + aa[gg].annotations[res].description +\r
+ "<br>");\r
+ }\r
+ }\r
+ if (tip.length() != 6)\r
+ {\r
+ tip.setLength(tip.length() - 4);\r
+ this.setToolTipText(tip.toString() + "</html>");\r
+ }\r
+ }\r
+ else if (aa[row].annotations[res] != null\r
+ && aa[row].annotations[res].description != null)\r
+ {\r
+ this.setToolTipText(aa[row].annotations[res].description);\r
+ }\r
\r
- if (aa[row].annotations[res].description != null)\r
- text.append(" " + aa[row].annotations[res].description);\r
+ if (aa[row].annotations[res] != null)\r
+ {\r
+ StringBuffer text = new StringBuffer("Sequence position " +\r
+ (res + 1));\r
\r
- ap.alignFrame.statusBar.setText(text.toString());\r
- }\r
+ if (aa[row].annotations[res].description != null)\r
+ {\r
+ text.append(" " + aa[row].annotations[res].description);\r
}\r
- else\r
- this.setToolTipText(null);\r
- }\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\r
- */\r
- public void mouseClicked(MouseEvent evt)\r
+ ap.alignFrame.statusBar.setText(text.toString());\r
+ }\r
+ }\r
+ else\r
{\r
+ this.setToolTipText(null);\r
}\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param g DOCUMENT ME!\r
- */\r
- public void paintComponent(Graphics g)\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
+ public void mouseClicked(MouseEvent evt)\r
+ {\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param g DOCUMENT ME!\r
+ */\r
+ public void paintComponent(Graphics g)\r
+ {\r
+ g.setColor(Color.white);\r
+ g.fillRect(0, 0, getWidth(), getHeight());\r
+\r
+ if (image != null)\r
{\r
- g.setColor(Color.white);\r
- g.fillRect(0, 0, getWidth(), getHeight());\r
-\r
- if(image!=null)\r
- {if (fastPaint\r
- || (getVisibleRect().width != g.getClipBounds().width)\r
- || (getVisibleRect().height != g.getClipBounds().height))\r
- {\r
- g.drawImage(image, 0, 0, this);\r
- fastPaint = false;\r
- return;\r
- }\r
+ if (fastPaint\r
+ || (getVisibleRect().width != g.getClipBounds().width)\r
+ || (getVisibleRect().height != g.getClipBounds().height))\r
+ {\r
+ g.drawImage(image, 0, 0, this);\r
+ fastPaint = false;\r
+ return;\r
}\r
- imgWidth = (av.endRes - av.startRes + 1) * av.charWidth;\r
+ }\r
+ imgWidth = (av.endRes - av.startRes + 1) * av.charWidth;\r
\r
- if (image == null || imgWidth != image.getWidth()\r
- || image.getHeight(this) != getHeight())\r
- {\r
- image = new BufferedImage(imgWidth, ap.annotationPanel.getHeight(),\r
- BufferedImage.TYPE_INT_RGB);\r
- gg = (Graphics2D) image.getGraphics();\r
+ if (image == null || imgWidth != image.getWidth()\r
+ || image.getHeight(this) != getHeight())\r
+ {\r
+ image = new BufferedImage(imgWidth, ap.annotationPanel.getHeight(),\r
+ BufferedImage.TYPE_INT_RGB);\r
+ gg = (Graphics2D) image.getGraphics();\r
\r
- if(av.antiAlias)\r
+ if (av.antiAlias)\r
+ {\r
gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
RenderingHints.VALUE_ANTIALIAS_ON);\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
- drawComponent(gg, av.startRes, av.endRes + 1);\r
- g.drawImage(image, 0, 0, this);\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
- * DOCUMENT ME!\r
- *\r
- * @param horizontal DOCUMENT ME!\r
- */\r
- public void fastPaint(int horizontal)\r
+ drawComponent(gg, av.startRes, av.endRes + 1);\r
+ g.drawImage(image, 0, 0, this);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param horizontal DOCUMENT ME!\r
+ */\r
+ public void fastPaint(int horizontal)\r
+ {\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
- 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
+ repaint();\r
+ return;\r
+ }\r
\r
- gg.copyArea(0, 0, imgWidth, getHeight(), -horizontal * av.charWidth, 0);\r
+ gg.copyArea(0, 0, imgWidth, getHeight(), -horizontal * av.charWidth, 0);\r
\r
- int sr = av.startRes;\r
- int er = av.endRes + 1;\r
- int transX = 0;\r
+ int sr = av.startRes;\r
+ int er = av.endRes + 1;\r
+ int 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
+ 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
+ gg.translate(transX, 0);\r
\r
- drawComponent(gg, sr, er);\r
+ drawComponent(gg, sr, er);\r
\r
- gg.translate(-transX, 0);\r
+ gg.translate( -transX, 0);\r
\r
- fastPaint = true;\r
+ fastPaint = true;\r
\r
- repaint();\r
+ repaint();\r
\r
- }\r
+ }\r
\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
+ * 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
+ if (av.updatingConsensus || av.updatingConservation)\r
{\r
- if(av.updatingConsensus || av.updatingConservation)\r
+ if (image == null)\r
{\r
- if(image==null)\r
- {\r
- return;\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
+ return;\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
+ Graphics2D fadedG = (Graphics2D) fadedImage.getGraphics();\r
\r
- fadedG.setColor(Color.white);\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
+ fadedG.setComposite(\r
+ AlphaComposite.getInstance(\r
+ AlphaComposite.SRC_OVER, .3f));\r
+ fadedG.drawImage(image, 0, 0, this);\r
\r
}\r
- else\r
- fadedImage = null;\r
\r
+ }\r
+ else\r
+ {\r
+ fadedImage = null;\r
+ }\r
\r
- g.setColor(Color.white);\r
- g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight());\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
+ g.setFont(av.getFont());\r
+ if (fm == null)\r
+ {\r
+ fm = g.getFontMetrics();\r
+ }\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
+ if (av.validCharWidth)\r
+ {\r
+ g.drawString("Alignment has no annotations", 20, 15);\r
+ }\r
\r
+ return;\r
+ }\r
\r
+ AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\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
- if(av.validCharWidth)\r
- g.drawString("Alignment has no annotations", 20, 15);\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
- return;\r
- }\r
+ boolean[] graphGroupDrawn = new boolean[aa.length];\r
\r
+ //\u03B2 \u03B1\r
+ for (int i = 0; i < aa.length; i++)\r
+ {\r
+ AlignmentAnnotation row = aa[i];\r
\r
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
+ if (!row.visible)\r
+ {\r
+ continue;\r
+ }\r
\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
+ lastSS = ' ';\r
+ lastSSX = 0;\r
\r
- boolean [] graphGroupDrawn = new boolean[aa.length];\r
+ if (row.graph > 0)\r
+ {\r
+ if (row.graphGroup > -1 && graphGroupDrawn[row.graphGroup])\r
+ {\r
+ continue;\r
+ }\r
\r
+ // this is so that we draw the characters below the graph\r
+ y += row.height;\r
\r
- //\u03B2 \u03B1\r
- for (int i = 0; i < aa.length; i++)\r
+ if (row.hasText)\r
{\r
- AlignmentAnnotation row = aa[i];\r
+ y -= av.charHeight;\r
+ }\r
+ }\r
\r
- if (!row.visible)\r
- {\r
- continue;\r
- }\r
+ if (av.updatingConsensus && aa[i] == av.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
- lastSS = ' ';\r
- lastSSX = 0;\r
+ continue;\r
+ }\r
+ else if (av.updatingConservation && aa[i].label.equals("Conservation"))\r
+ {\r
\r
- if (row.graph>0)\r
- {\r
- if(row.graphGroup>-1 && graphGroupDrawn[ row.graphGroup ] )\r
- continue;\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
- // this is so that we draw the characters below the graph\r
- y += row.height;\r
+ g.setColor(Color.black);\r
+ // g.drawString("Calculating Conservation.....",20, y-row.height/2);\r
\r
- if (row.hasText)\r
- {\r
- y -= av.charHeight;\r
- }\r
- }\r
+ continue;\r
+ }\r
+ else if (av.updatingConservation && aa[i].label.equals("Quality"))\r
+ {\r
\r
- if (av.updatingConsensus && aa[i]==av.consensus)\r
- {\r
- y += av.charHeight;\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
- 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
+ continue;\r
+ }\r
\r
- continue;\r
- }\r
- else if (av.updatingConservation && aa[i].label.equals("Conservation"))\r
- {\r
+ if (row.hasText)\r
+ {\r
+ iconOffset = av.charHeight / 2 + 4;\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
+ {\r
+ column = startRes + x;\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
+ if ( (row.annotations.length <= column) ||\r
+ (row.annotations[column] == null))\r
+ {\r
+ validRes = false;\r
+ }\r
+ else\r
+ {\r
+ validRes = true;\r
+ }\r
\r
- g.setColor(Color.black);\r
- // g.drawString("Calculating Conservation.....",20, y-row.height/2);\r
+ if (activeRow == i)\r
+ {\r
+ g.setColor(Color.red);\r
\r
- continue;\r
- }\r
- else if (av.updatingConservation && aa[i].label.equals("Quality"))\r
+ if (av.getColumnSelection() != null)\r
+ {\r
+ for (int n = 0; n < av.getColumnSelection().size(); n++)\r
{\r
+ int v = av.getColumnSelection().columnAt(n);\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
+ if (v == column)\r
+ {\r
+ g.fillRect(x * av.charWidth, y,\r
+ av.charWidth, av.charHeight);\r
+ }\r
}\r
+ }\r
+ }\r
\r
+ if (av.validCharWidth && validRes &&\r
+ (row.annotations[column].displayCharacter.length() > 0))\r
+ {\r
\r
- if (row.hasText)\r
- {\r
- iconOffset = av.charHeight / 2 + 4;\r
- }\r
- else\r
- {\r
- iconOffset = 0;\r
- }\r
+ int charOffset = (av.charWidth -\r
+ fm.charWidth(row.annotations[column].\r
+ 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);\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);\r
+ }\r
+ }\r
\r
- x = 0;\r
- while (x < endRes-startRes)\r
+ if (row.hasIcons)\r
+ {\r
+ if (!validRes ||\r
+ (row.annotations[column].secondaryStructure != lastSS))\r
+ {\r
+ switch (lastSS)\r
{\r
- if (av.hasHiddenColumns)\r
- {\r
- column = av.getColumnSelection().adjustForHiddenColumns(startRes+x);\r
- if (column > row.annotations.length-1)\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
- else\r
- column = startRes+x;\r
\r
+ int sCol = (lastSSX / av.charWidth) + startRes;\r
+ int x1 = lastSSX;\r
+ int x2 = (x * av.charWidth);\r
\r
- if ((row.annotations.length <= column) ||\r
- (row.annotations[column] == null))\r
- {\r
- validRes = false;\r
- }\r
- else\r
+ if (sCol == 0 ||\r
+ row.annotations[sCol - 1] == null ||\r
+ row.annotations[sCol - 1].secondaryStructure != 'H')\r
{\r
- validRes = true;\r
+ g.fillArc(lastSSX, y + 4 + iconOffset, av.charWidth, 8, 90,\r
+ 180);\r
+ x1 += av.charWidth / 2;\r
}\r
\r
-\r
- if (activeRow == i)\r
+ if (row.annotations[column] == null ||\r
+ row.annotations[column].secondaryStructure != 'H')\r
{\r
- g.setColor(Color.red);\r
-\r
- if (av.getColumnSelection() != null)\r
- {\r
- for (int n = 0; n < av.getColumnSelection().size(); n++)\r
- {\r
- int v = av.getColumnSelection().columnAt(n);\r
-\r
- if (v == column)\r
- {\r
- g.fillRect(x * av.charWidth, y,\r
- av.charWidth, av.charHeight);\r
- }\r
- }\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
- if (av.validCharWidth && validRes &&\r
- (row.annotations[column].displayCharacter.length() > 0))\r
- {\r
+ g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);\r
+ break;\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 );\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 );\r
- }\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[]\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 + 8 + iconOffset\r
+ }, 3);\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
+ break;\r
\r
+ default:\r
+ g.setColor(Color.gray);\r
+ g.fillRect(lastSSX, y + 6 + iconOffset,\r
+ (x * av.charWidth) - lastSSX, 2);\r
\r
- column++;\r
- x++;\r
+ break;\r
}\r
\r
- if(column>=row.annotations.length)\r
- column = row.annotations.length-1;\r
+ if (validRes)\r
+ {\r
+ lastSS = row.annotations[column].secondaryStructure;\r
+ }\r
+ else\r
+ {\r
+ lastSS = ' ';\r
+ }\r
\r
- // x ++;\r
+ lastSSX = (x * av.charWidth);\r
+ }\r
+ }\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
+ column++;\r
+ x++;\r
+ }\r
\r
- break;\r
+ if (column >= row.annotations.length)\r
+ {\r
+ column = row.annotations.length - 1;\r
+ }\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
+ // x ++;\r
\r
- default:\r
- g.setColor(Color.gray);\r
- g.fillRect(lastSSX, y + 6 + iconOffset,\r
- (x*av.charWidth) - lastSSX, 2);\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
- break;\r
- }\r
- }\r
+ int sCol = (lastSSX / av.charWidth) + startRes;\r
+ int x1 = lastSSX;\r
+ int x2 = (x * av.charWidth);\r
\r
- if (row.graph>0 && row.graphHeight>0)\r
+ if (sCol == 0 ||\r
+ row.annotations[sCol - 1] == null ||\r
+ row.annotations[sCol - 1].secondaryStructure != 'H')\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
+ g.fillArc(lastSSX, y + 4 + iconOffset, av.charWidth, 8, 90, 180);\r
+ x1 += av.charWidth / 2;\r
}\r
\r
- if (row.graph>0 && row.hasText)\r
+ if (row.annotations[column] == null ||\r
+ row.annotations[column].secondaryStructure != 'H')\r
{\r
- y += av.charHeight;\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
- if (row.graph==0)\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
- y += aa[i].height;\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, y + 6 + iconOffset,\r
+ (x * av.charWidth) - lastSSX, 2);\r
+\r
+ break;\r
}\r
- }\r
+ }\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
- if(sRes>aa.annotations.length)\r
- return;\r
+ if (row.graph > 0 && row.graphHeight > 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
+ {\r
+ continue;\r
+ }\r
\r
+ if (aa[gg] != row)\r
+ {\r
+ aa[gg].visible = false;\r
+ }\r
\r
- int x = 0;\r
+ if (aa[gg].graphMax > groupmax)\r
+ {\r
+ groupmax = aa[gg].graphMax;\r
+ }\r
+ if (aa[gg].graphMin < groupmin)\r
+ {\r
+ groupmin = aa[gg].graphMin;\r
+ }\r
+ }\r
\r
- //Adjustment for fastpaint to left\r
- if(eRes<av.endRes)\r
- eRes++;\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
- eRes = Math.min(eRes, aa.annotations.length);\r
+ graphGroupDrawn[row.graphGroup] = true;\r
+ }\r
+ else\r
+ {\r
+ drawLineGraph(g, row, startRes, endRes,\r
+ y, row.graphMin, row.graphMax, row.graphHeight);\r
+ }\r
+ }\r
+ else if (row.graph == AlignmentAnnotation.BAR_GRAPH)\r
+ {\r
+ drawBarGraph(g, row, startRes, endRes,\r
+ row.graphMin, row.graphMax, y);\r
+ }\r
+ }\r
\r
- if(sRes==0)\r
+ if (row.graph > 0 && row.hasText)\r
{\r
- x++;\r
+ y += av.charHeight;\r
}\r
\r
- int y1=y, y2=y;\r
- float range = max - min;\r
+ if (row.graph == 0)\r
+ {\r
+ y += aa[i].height;\r
+ }\r
+ }\r
+ }\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
+ if (sRes > aa.annotations.length)\r
+ {\r
+ return;\r
+ }\r
\r
- ////Draw origin\r
- if(min<0)\r
- y2 = y - (int)((0-min / range)*graphHeight);\r
+ int x = 0;\r
\r
- g.setColor(Color.gray);\r
- g.drawLine(x-av.charWidth,y2,(eRes-sRes+1)*av.charWidth,y2);\r
+ //Adjustment for fastpaint to left\r
+ if (eRes < av.endRes)\r
+ {\r
+ eRes++;\r
+ }\r
\r
- eRes = Math.min(eRes, aa.annotations.length);\r
+ eRes = Math.min(eRes, aa.annotations.length);\r
\r
- int column;\r
- int aaMax = aa.annotations.length-1;\r
+ if (sRes == 0)\r
+ {\r
+ x++;\r
+ }\r
\r
- while( x < eRes - sRes )\r
- {\r
- column = sRes + x;\r
- if(av.hasHiddenColumns)\r
- {\r
- column = av.getColumnSelection().adjustForHiddenColumns(column);\r
- }\r
+ int y1 = y, y2 = y;\r
+ float range = max - min;\r
\r
- if (column > aaMax)\r
- {\r
- break;\r
- }\r
+ ////Draw origin\r
+ if (min < 0)\r
+ {\r
+ y2 = y - (int) ( (0 - min / range) * graphHeight);\r
+ }\r
\r
- if(aa.annotations[column]==null || aa.annotations[column-1]==null)\r
- {\r
- x++;\r
- continue;\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
- 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
+ int column;\r
+ int aaMax = aa.annotations.length - 1;\r
\r
- g.drawLine(x*av.charWidth-av.charWidth/2, y1, x*av.charWidth+av.charWidth/2, y2);\r
- x ++;\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
- 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
+ if (column > aaMax)\r
+ {\r
+ break;\r
+ }\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
+ if (aa.annotations[column] == null || aa.annotations[column - 1] == null)\r
+ {\r
+ x++;\r
+ continue;\r
}\r
+\r
+ g.setColor(aa.annotations[column].colour);\r
+ y1 = y -\r
+ (int) ( ( (aa.annotations[column - 1].value - min) / range) * graphHeight);\r
+ y2 = y -\r
+ (int) ( ( (aa.annotations[column].value - min) / range) * graphHeight);\r
+\r
+ g.drawLine(x * av.charWidth - av.charWidth / 2, y1,\r
+ x * av.charWidth + av.charWidth / 2, y2);\r
+ x++;\r
}\r
\r
- public void drawBarGraph(Graphics g, AlignmentAnnotation aa,\r
- int sRes, int eRes,\r
- float min, float max,\r
- int y)\r
+ if (aa.threshold != null)\r
{\r
- if(sRes>aa.annotations.length)\r
- return;\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[]\r
+ {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
+ int sRes, int eRes,\r
+ float min, float max,\r
+ int y)\r
+ {\r
+ if (sRes > aa.annotations.length)\r
+ {\r
+ return;\r
+ }\r
\r
- eRes = Math.min(eRes, aa.annotations.length);\r
+ eRes = Math.min(eRes, aa.annotations.length);\r
\r
- int x=0, y1=y, y2=y;\r
+ int x = 0, y1 = y, y2 = y;\r
\r
- float range = max - min;\r
+ float range = max - min;\r
\r
- if(min<0)\r
- y2 = y - (int)((0-min / (range))*aa.graphHeight);\r
+ if (min < 0)\r
+ {\r
+ y2 = y - (int) ( (0 - min / (range)) * aa.graphHeight);\r
+ }\r
\r
- g.setColor(Color.gray);\r
+ g.setColor(Color.gray);\r
\r
- g.drawLine(x,y2,(eRes-sRes)*av.charWidth,y2);\r
+ g.drawLine(x, y2, (eRes - sRes) * av.charWidth, y2);\r
\r
- int column;\r
- int aaMax = aa.annotations.length-1;\r
+ int column;\r
+ int aaMax = aa.annotations.length - 1;\r
\r
- while( x < eRes-sRes )\r
+ while (x < eRes - sRes)\r
+ {\r
+ column = sRes + x;\r
+ if (av.hasHiddenColumns)\r
{\r
- column = sRes + x;\r
- if(av.hasHiddenColumns)\r
- {\r
- column = av.getColumnSelection().adjustForHiddenColumns(column);\r
- }\r
-\r
- if(column > aaMax)\r
- {\r
- break;\r
- }\r
-\r
- if (aa.annotations[column] == null)\r
- {\r
- x ++;\r
- continue;\r
- }\r
+ column = av.getColumnSelection().adjustForHiddenColumns(column);\r
+ }\r
\r
- g.setColor(aa.annotations[column].colour);\r
- y1 = y - (int) (((aa.annotations[column].value-min) / (range)) * aa.graphHeight);\r
+ if (column > aaMax)\r
+ {\r
+ break;\r
+ }\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
+ if (aa.annotations[column] == null)\r
+ {\r
+ x++;\r
+ continue;\r
+ }\r
\r
- x ++ ;\r
+ g.setColor(aa.annotations[column].colour);\r
+ y1 = y -\r
+ (int) ( ( (aa.annotations[column].value - min) / (range)) * aa.graphHeight);\r
\r
+ if (y1 - y2 > 0)\r
+ {\r
+ g.fillRect(x * av.charWidth, y2, av.charWidth, y1 - y2);\r
}\r
- if(aa.threshold!=null)\r
+ else\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
+ g.fillRect(x * av.charWidth, y1, av.charWidth, y2 - y1);\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
+ x++;\r
+\r
+ }\r
+ if (aa.threshold != null)\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
+ 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[]\r
+ {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
- int x = 0, height;\r
+ // used by overview window\r
+ public void drawGraph(Graphics g, AlignmentAnnotation aa, int width, int y,\r
+ 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
+ int x = 0, height;\r
\r
- height = (int) ( (aa.annotations[j].value / aa.graphMax) * y);\r
- if (height > y)\r
- height = y;\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
- g.fillRect(x, y - height, av.charWidth, height);\r
+ height = (int) ( (aa.annotations[j].value / aa.graphMax) * y);\r
+ if (height > y)\r
+ {\r
+ height = y;\r
}\r
- x += av.charWidth;\r
+\r
+ g.fillRect(x, y - height, av.charWidth, height);\r
}\r
+ x += av.charWidth;\r
}\r
+ }\r
\r
}\r
git://source.jalview.org / jalview.git / blobdiff