+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 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
package jalview.gui;\r
\r
import jalview.datamodel.*;\r
\r
-import javax.swing.*;\r
import java.awt.*;\r
import java.awt.event.*;\r
-import java.util.*;\r
import java.awt.image.*;\r
\r
-public class AnnotationPanel extends JPanel implements MouseListener, MouseMotionListener, ActionListener, AdjustmentListener\r
-{\r
- AlignViewport av;\r
- AlignmentPanel ap;\r
- int activeRow =-1;\r
+import javax.swing.*;\r
\r
- ArrayList 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 Color HELIX_COLOUR = Color.red.darker();\r
- static Color SHEET_COLOUR = Color.green.darker().darker();\r
\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class AnnotationPanel 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
+ 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
+ /**\r
+ * Creates a new AnnotationPanel object.\r
+ *\r
+ * @param ap DOCUMENT ME!\r
+ */\r
+ public AnnotationPanel(AlignmentPanel ap)\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
- BufferedImage image;\r
- Graphics2D gg;\r
- FontMetrics fm;\r
- int imgWidth=0;\r
+ public AnnotationPanel(AlignViewport av)\r
+ {\r
+ this.av = av;\r
+ }\r
\r
- boolean fastPaint = false;\r
\r
- public static int GRAPH_HEIGHT = 40;\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
+ image = null;\r
+ AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
+ int height = 0;\r
\r
+ if (aa != null)\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
+\r
+ if (aa[i].graph>0)\r
+ {\r
+ aa[i].height += aa[i].graphHeight;\r
+ }\r
+\r
+ if (aa[i].height == 0)\r
+ {\r
+ aa[i].height = 20;\r
+ }\r
+\r
+ height += aa[i].height;\r
+ }\r
+ }\r
+ else\r
+ {\r
+ height = 20;\r
+ }\r
\r
- public AnnotationPanel(AlignmentPanel ap)\r
- {\r
- this.ap = ap;\r
- av = ap.av;\r
- this.setLayout(null);\r
- addMouseListener(this);\r
- addMouseMotionListener(this);\r
- adjustPanelHeight();\r
+ this.setPreferredSize(new Dimension(1, height));\r
\r
+ return height;\r
+ }\r
\r
- ap.annotationScroller.getVerticalScrollBar().addAdjustmentListener( this );\r
- }\r
\r
- public void adjustmentValueChanged(AdjustmentEvent evt)\r
- {\r
- ap.alabels.setScrollOffset( -evt.getValue() );\r
- }\r
\r
- public void adjustPanelHeight()\r
- {\r
- // setHeight of panels\r
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
- int height = 0;\r
- if(aa!=null)\r
- for (int i = 0; i < aa.length; i++)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
+ public void actionPerformed(ActionEvent evt)\r
{\r
- if(!aa[i].visible)\r
- continue;\r
+ AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
+ Annotation[] anot = aa[activeRow].annotations;\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
+ if (label == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ if ((label.length() > 0) && !aa[activeRow].hasText)\r
+ {\r
+ aa[activeRow].hasText = true;\r
+ }\r
+\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
+ anot[index] = new Annotation(label, "", ' ', 0);\r
+ }\r
+\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", Color.black);\r
\r
- aa[i].height = 0;\r
+ for (int i = 0; i < av.getColumnSelection().size(); i++)\r
+ {\r
+ int index = av.getColumnSelection().columnAt(i);\r
\r
- if(aa[i].hasText)\r
- aa[i].height += av.charHeight;\r
- if (aa[i].hasIcons)\r
- aa[i].height += 16;\r
+ if (anot[index] == null)\r
+ {\r
+ anot[index] = new Annotation("", "", ' ', 0);\r
+ }\r
\r
- if (aa[i].isGraph)\r
- aa[i].height += GRAPH_HEIGHT;\r
+ anot[index].colour = col;\r
+ }\r
+ }\r
+ else // HELIX OR SHEET\r
+ {\r
+ char type = 0;\r
+ String symbol = "\u03B1";\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
+ if (!aa[activeRow].hasIcons)\r
+ {\r
+ aa[activeRow].hasIcons = true;\r
+ }\r
+\r
+ String label = JOptionPane.showInputDialog("Enter a label for the structure?",\r
+ symbol);\r
+\r
+ if (label == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ if ((label.length() > 0) && !aa[activeRow].hasText)\r
+ {\r
+ aa[activeRow].hasText = true;\r
+ }\r
+\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
+ anot[index] = new Annotation(label, "", type, 0);\r
+ }\r
+\r
+ anot[index].secondaryStructure = type;\r
+ anot[index].displayCharacter = label;\r
+ }\r
+ }\r
\r
- if(aa[i].height==0)\r
- aa[i].height = 20;\r
- height += aa[i].height;\r
- }\r
- else height=20;\r
- this.setPreferredSize(new Dimension(1, height));\r
+ adjustPanelHeight();\r
+ repaint();\r
\r
- }\r
+ return;\r
+ }\r
\r
- public void addEditableColumn(int i)\r
- {\r
- if(activeRow==-1)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
+ public void mousePressed(MouseEvent evt)\r
{\r
- AlignmentAnnotation [] aa = av.alignment.getAlignmentAnnotation();\r
- for(int j=0; j<aa.length; j++)\r
- if(aa[j].editable)\r
+ int height = 0;\r
+ activeRow = -1;\r
+\r
+ AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
+ if(aa==null)\r
+ return;\r
+\r
+ for (int i = 0; i < aa.length; i++)\r
{\r
- activeRow = j;\r
- break;\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
- }\r
\r
- if(activeRes==null)\r
- {\r
- activeRes = new ArrayList();\r
- activeRes.add(String.valueOf(i));\r
- return;\r
- }\r
+ if (SwingUtilities.isRightMouseButton(evt))\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
+ }\r
\r
- activeRes.add(String.valueOf(i));\r
+ if (aa == null)\r
+ {\r
+ return;\r
+ }\r
\r
- }\r
+ int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();\r
\r
+ min = res;\r
+ max = res;\r
\r
- public void actionPerformed(ActionEvent evt)\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
\r
- AlignmentAnnotation [] aa = av.alignment.getAlignmentAnnotation();\r
- Annotation [] anot = aa[activeRow].annotations;\r
+ for (int i = 0; i < av.alignment.getSequences().size(); i++)\r
+ {\r
+ sg.addSequence(av.alignment.getSequenceAt(i), false);\r
+ }\r
\r
- if(evt.getActionCommand().equals(REMOVE))\r
- {\r
- for(int i=0; i<activeRes.size(); i++)\r
- {\r
- anot[Integer.parseInt(activeRes.get(i).toString())] = null;\r
- anot[Integer.parseInt(activeRes.get(i).toString())] = null;\r
- }\r
- }\r
- else if(evt.getActionCommand().equals(LABEL))\r
- {\r
- String label = JOptionPane.showInputDialog(this, "Enter Label ", "Enter label", JOptionPane.QUESTION_MESSAGE );\r
- if(label==null)\r
- label = "";\r
+ sg.setStartRes(res);\r
+ sg.setEndRes(res);\r
+ av.setSelectionGroup(sg);\r
+ }\r
\r
- if(label.length()>0 && !aa[activeRow].hasText)\r
- aa[activeRow].hasText = true;\r
+ ap.repaint();\r
\r
- for(int i=0; i<activeRes.size(); i++)\r
- {\r
- int index = Integer.parseInt(activeRes.get(i).toString());\r
- if(anot[index]==null)\r
- anot[index] = new Annotation(label, "", ' ',0);\r
- anot[index].displayCharacter = label;\r
- }\r
}\r
- else if(evt.getActionCommand().equals(COLOUR))\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
+ public void mouseReleased(MouseEvent evt)\r
{\r
- Color col = JColorChooser.showDialog(this, "Choose foreground colour", Color.black);\r
- for (int i = 0; i < activeRes.size(); i++)\r
- {\r
- int index = Integer.parseInt(activeRes.get(i).toString());\r
- if (anot[index] == null)\r
- anot[index] = new Annotation("", "", ' ', 0);\r
- anot[index].colour = col;\r
- }\r
+ graphStretch = -1;\r
+ graphStretchY = -1;\r
+ mouseDragging = false;\r
}\r
- else // HELIX OR SHEET\r
- {\r
- char type = 0;\r
- String symbol = "\u03B1";\r
- if(evt.getActionCommand().equals(HELIX))\r
- type = 'H';\r
- else if(evt.getActionCommand().equals(SHEET))\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
+ public void mouseEntered(MouseEvent evt)\r
{\r
- type = 'E';\r
- symbol = "\u03B2";\r
+ if(mouseDragging)\r
+ ap.seqPanel.scrollCanvas(null);\r
}\r
\r
- if(!aa[activeRow].hasIcons)\r
- aa[activeRow].hasIcons = true;\r
-\r
-\r
- String label = JOptionPane.showInputDialog("Enter a label for the structure?", symbol );\r
- if(label==null)\r
- label="";\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
+ public void mouseExited(MouseEvent evt)\r
+ {\r
+ if(mouseDragging)\r
+ ap.seqPanel.scrollCanvas(evt);\r
+ }\r
\r
- if(label.length()>0 && !aa[activeRow].hasText)\r
- aa[activeRow].hasText = true;\r
\r
- for(int i=0; i<activeRes.size(); i++)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
+ public void mouseDragged(MouseEvent evt)\r
{\r
- int index = Integer.parseInt(activeRes.get(i).toString());\r
- if (anot[index] == null)\r
+ if(graphStretch>-1)\r
{\r
- anot[index] = new Annotation(label, "", type, 0);\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
+ graphStretchY = evt.getY();\r
+ adjustPanelHeight();\r
+ ap.repaint();\r
}\r
+ else\r
+ {\r
+ mouseDragging = true;\r
\r
- anot[ index ].secondaryStructure = type;\r
- anot[ index ].displayCharacter = label;\r
- }\r
- }\r
+ int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();\r
\r
- adjustPanelHeight();\r
- activeRes = null;\r
- repaint();\r
- return;\r
+ SequenceGroup sg = av.getSelectionGroup();\r
\r
+ if (res < min)\r
+ {\r
+ min = res;\r
+ }\r
\r
- }\r
+ if (res > max)\r
+ {\r
+ max = res;\r
+ }\r
\r
- public void mousePressed(MouseEvent evt)\r
- {\r
- if (SwingUtilities.isRightMouseButton(evt))\r
- {\r
- if(activeRes==null)\r
- return;\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
- 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
- return;\r
+ }\r
}\r
\r
-\r
- AlignmentAnnotation [] aa = av.alignment.getAlignmentAnnotation();\r
- if(aa==null)\r
- return;\r
-\r
- int height = 0;\r
- activeRow = -1;\r
- for(int i=0; i<aa.length; i++)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
+ public void mouseMoved(MouseEvent evt)\r
{\r
- height+= aa[i].height;\r
+ AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
\r
- if(evt.getY()<height)\r
- {\r
- if(!aa[i].editable)\r
+ if (aa == null)\r
{\r
- activeRes = null;\r
- continue;\r
+ return;\r
}\r
\r
- activeRow = i;\r
- break;\r
- }\r
- }\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
\r
- int res = evt.getX() / av.getCharWidth() + av.getStartRes();\r
+ if (evt.getY() < height)\r
+ {\r
+ row = i;\r
\r
- if(evt.isControlDown() || evt.isAltDown())\r
- addEditableColumn(res);\r
+ break;\r
+ }\r
+ }\r
\r
- else if(evt.isShiftDown())\r
- {\r
+ int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();\r
\r
- if(activeRes==null)\r
- activeRes=new ArrayList();\r
- else\r
- {\r
- int start = Integer.parseInt( activeRes.get( activeRes.size()-1 ).toString() );\r
- int end = res;\r
- if(end<start)\r
- {\r
- int temp = end;\r
- end = start;\r
- start = temp;\r
- }\r
- for(int n=start; n<=end; n++)\r
- addEditableColumn(n);\r
+ if(av.hasHiddenColumns)\r
+ res = av.getColumnSelection().adjustForHiddenColumns(res);\r
\r
- }\r
+ if (row > -1 && res<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[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
+ 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
+ aa[row].annotations[res].description);\r
+\r
+ ap.alignFrame.statusBar.setText(text.toString());\r
+ }\r
+ }\r
}\r
- else\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
+ public void mouseClicked(MouseEvent evt)\r
{\r
- activeRes = new ArrayList();\r
- activeRes.add( String.valueOf(res) );\r
}\r
\r
- repaint();\r
-\r
- }\r
- public void mouseReleased(MouseEvent evt)\r
- { }\r
- public void mouseEntered(MouseEvent evt)\r
- { }\r
- public void mouseExited(MouseEvent evt)\r
- { }\r
- public void mouseDragged(MouseEvent evt)\r
- { }\r
- public void mouseMoved(MouseEvent evt)\r
- {\r
- ToolTipManager.sharedInstance().registerComponent(this);\r
- AlignmentAnnotation [] aa = av.alignment.getAlignmentAnnotation();\r
- if(aa==null)\r
- return;\r
-\r
- int row = -1;\r
- int height=0;\r
- for(int i=0; i<aa.length; i++)\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( aa[i].visible )\r
- height += aa[i].height;\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
+ }\r
+ imgWidth = (av.endRes - av.startRes + 1) * av.charWidth;\r
\r
- if(evt.getY()<height)\r
+ if (image == null || imgWidth != image.getWidth()\r
+ || image.getHeight(this) != getHeight())\r
{\r
- row = i;\r
- break;\r
+ image = new BufferedImage(imgWidth, ap.annotationPanel.getHeight(),\r
+ BufferedImage.TYPE_INT_RGB);\r
+ gg = (Graphics2D) image.getGraphics();\r
+\r
+ if(av.antiAlias)\r
+ gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
+ RenderingHints.VALUE_ANTIALIAS_ON);\r
+\r
+ gg.setFont(av.getFont());\r
+ fm = gg.getFontMetrics();\r
}\r
+\r
+\r
+ drawComponent(gg, av.startRes, av.endRes + 1);\r
+ g.drawImage(image, 0, 0, this);\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
- this.setToolTipText(aa[row].annotations[res].description);\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param horizontal DOCUMENT ME!\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
+ {\r
+ repaint();\r
+ return;\r
+ }\r
\r
- }\r
- public void mouseClicked(MouseEvent evt) {}\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
\r
- public void paintComponent(Graphics g)\r
- {\r
- g.setColor(Color.white);\r
- g.fillRect(0,0,getWidth(), getHeight());\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
- if(fastPaint)\r
- {\r
- g.drawImage(image, 0, 0, this);\r
- fastPaint = false;\r
- return;\r
- }\r
+ gg.translate(transX, 0);\r
\r
- imgWidth = (av.endRes-av.startRes+1) *av.charWidth;\r
+ drawComponent(gg, sr, er);\r
\r
- image = new BufferedImage(imgWidth,\r
- ap.annotationPanel.getHeight(),\r
- BufferedImage.TYPE_INT_RGB);\r
- gg = (Graphics2D) image.getGraphics();\r
- gg.setColor(Color.white);\r
- gg.fillRect(0, 0, imgWidth, getHeight());\r
- gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
- RenderingHints.VALUE_ANTIALIAS_ON);\r
- fm = gg.getFontMetrics();\r
- gg.setFont(av.getFont());\r
+ gg.translate(-transX, 0);\r
\r
+ fastPaint = true;\r
\r
- drawComponent( gg, av.startRes, av.endRes+1);\r
- g.drawImage( image, 0, 0, this);\r
- }\r
+ repaint();\r
\r
- public void fastPaint(int horizontal)\r
-{\r
- if(image==null || horizontal ==0)\r
- {\r
- repaint();\r
- return;\r
- }\r
+ }\r
\r
- gg.copyArea( 0,0, imgWidth, getHeight(), -horizontal*av.charWidth, 0 );\r
- int sr=av.startRes, er=av.endRes+1, transX=0;\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
+ g.setFont(av.getFont());\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 (fm == null)\r
+ fm = g.getFontMetrics();\r
\r
\r
- gg.translate(transX, 0);\r
+ g.setColor(Color.white);\r
+ g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight());\r
\r
- drawComponent(gg, sr, er);\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
\r
- gg.translate( -transX, 0 );\r
+ return;\r
+ }\r
\r
- fastPaint = true;\r
- repaint();\r
-}\r
+ AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
\r
+ int x = 0;\r
+ int y = 0;\r
+ char lastSS;\r
+ int lastSSX;\r
+ int iconOffset = av.charHeight / 2;\r
+ boolean validRes = false;\r
\r
- public void drawComponent(Graphics2D g, int startRes, int endRes)\r
- {\r
- g.setColor(Color.white);\r
- g.fillRect(0,0,(endRes-startRes) *av.charWidth, getHeight());\r
- if(av.alignment.getAlignmentAnnotation()==null || av.alignment.getAlignmentAnnotation().length<1)\r
- {\r
- g.setColor(Color.black);\r
- g.drawString("Alignment has no annotations",20,15);\r
- return;\r
- }\r
+ boolean [] graphGroupDrawn = new boolean[aa.length];\r
\r
- AlignmentAnnotation [] aa = av.alignment.getAlignmentAnnotation();\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
- for(int i=0; i<aa.length; i++)\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
+\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
+ int column = startRes;\r
+ int yPos = startRes;\r
+\r
+ while (yPos < endRes)\r
+ {\r
+ if (av.hasHiddenColumns)\r
+ {\r
+ column = av.getColumnSelection().adjustForHiddenColumns(yPos);\r
+ if (column > row.annotations.length-1)\r
+ {\r
+ break;\r
+ }\r
+ }\r
+ else\r
+ column = yPos;\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
+ x = (yPos - startRes) * av.charWidth;\r
+\r
+ if (activeRow == i)\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((column - startRes) * av.charWidth, y,\r
+ av.charWidth, row.height);\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ if (validRes &&\r
+ (row.annotations[column].displayCharacter.length() > 0))\r
+ {\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, x+charOffset,\r
+ y + iconOffset + 3);\r
+ }\r
+ else if (((row.annotations[column - 1] == null)\r
+ ||\r
+ (!row.annotations[column].displayCharacter.equals(\r
+ row.annotations[column - 1].displayCharacter))))\r
+ {\r
+ g.drawString(row.annotations[column].displayCharacter, x+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
+ g.fillRoundRect(lastSSX, y + 4 + iconOffset,\r
+ x - lastSSX, 7, 8, 8);\r
+\r
+ break;\r
+\r
+ case 'E':\r
+ g.setColor(SHEET_COLOUR);\r
+ g.fillRect(lastSSX, y + 4 + iconOffset,\r
+ x - lastSSX - 4, 7);\r
+ g.fillPolygon(new int[] { x - 4, x - 4, x },\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 - 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;\r
+ }\r
+ }\r
+\r
+ yPos++;\r
+ }\r
+\r
+ x += av.charWidth;\r
+\r
+ if (row.hasIcons)\r
+ {\r
+ switch (lastSS)\r
+ {\r
+ case 'H':\r
+ g.setColor(HELIX_COLOUR);\r
+ g.fillRoundRect(lastSSX, y + 4 + iconOffset,\r
+ x - lastSSX, 7, 8, 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 - lastSSX - 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, y + 4 + iconOffset,\r
+ x - lastSSX, 7);\r
+\r
+ break;\r
+\r
+\r
+ default:\r
+ g.setColor(Color.gray);\r
+ g.fillRect(lastSSX, y + 6 + iconOffset, x - 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
+\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
- AlignmentAnnotation row = aa[i];\r
- if(!row.visible)\r
- continue;\r
+ if(sRes>aa.annotations.length)\r
+ return;\r
\r
- if(row.isGraph)\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
- }\r
- if(row.hasText)\r
- iconOffset = av.charHeight/2;\r
- else\r
- iconOffset = 0;\r
+ eRes = Math.min(eRes, aa.annotations.length);\r
\r
- for(j=startRes; j<endRes; j++)\r
- {\r
- validRes = row.annotations[j]==null?false:true;\r
+ int x = 0;\r
\r
- x = (j-startRes)*av.charWidth;\r
+ //Adjustment for fastpaint to left\r
+ if(eRes<av.endRes)\r
+ eRes++;\r
\r
+ if(sRes==0)\r
+ {\r
+ sRes++;\r
+ x+=av.charWidth;\r
+ }\r
\r
- if(activeRow==i)\r
- {\r
+ int y1=y, y2=y;\r
+ float range = max - min;\r
\r
- g.setColor(Color.red);\r
+ ////Draw origin\r
+ if(min<0)\r
+ y2 = (int)(y - (0-min / range)*graphHeight);\r
\r
- if(activeRes!=null)\r
- for (int n = 0; n < activeRes.size(); n++)\r
- {\r
- int v = Integer.parseInt(activeRes.get(n).toString()) ;\r
- if (v == j)\r
- g.fillRect( (j-startRes) * av.charWidth, y, av.charWidth, row.height);\r
- }\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 = sRes;\r
+ int yPos = sRes;\r
+ int aaMax = aa.annotations.length-1;\r
\r
- if(validRes && row.annotations[j].displayCharacter.length()>0)\r
- {\r
- int charOffset = (av.charWidth -\r
- fm.charWidth(row.annotations[j].displayCharacter.\r
- charAt(0))) / 2;\r
- g.setColor( row.annotations[j].colour);\r
- if(j==0)\r
+ while( yPos < eRes )\r
+ {\r
+ if(av.hasHiddenColumns)\r
+ {\r
+ column = av.getColumnSelection().adjustForHiddenColumns(yPos);\r
+ if(column > aaMax)\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
+ break;\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
+ else\r
+ column = yPos;\r
\r
- g.drawString(row.annotations[j].displayCharacter, x, y + iconOffset + 2);\r
+ yPos ++;\r
\r
- if(!row.hasIcons)\r
- g.drawString(row.annotations[j].displayCharacter, x + charOffset,\r
- y + iconOffset + 2);\r
- }\r
+ if(aa.annotations[column]==null || aa.annotations[column-1]==null)\r
+ {\r
+ x+=av.charWidth;\r
+ continue;\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
+ 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
+ g.drawLine(x-av.charWidth/2, y1, x+av.charWidth/2, y2);\r
+ x += av.charWidth;\r
}\r
-\r
- if (validRes && row.isGraph)\r
+ if(aa.threshold!=null)\r
{\r
- g.setColor(new Color(0,0,180));\r
- int height = (int)((row.annotations[j].value / row.graphMax)*GRAPH_HEIGHT);\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
- 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
+ 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
- total += row.annotations[i2].value;\r
- }\r
+ eRes = Math.min(eRes, aa.annotations.length);\r
\r
- total/=row.windowLength;\r
- height = (int)( (total / row.graphMax) *GRAPH_HEIGHT);\r
+ int x=0, y1, y2;\r
\r
- }\r
+ float range = max - min;\r
\r
- g.fillRect(x, y-height, av.charWidth, height );\r
- }\r
+ y1 = y2 = y;\r
\r
+ if(min<0)\r
+ y2 = (int)(y - (0-min / (range))*aa.graphHeight);\r
\r
- }\r
+ g.setColor(Color.gray);\r
+\r
+ g.drawLine(x,y2,(eRes-sRes)*av.charWidth,y2);\r
\r
- x+=av.charWidth;\r
\r
- if(row.hasIcons)\r
- switch (lastSS[i])\r
+ int column = sRes;\r
+ int yPos = sRes;\r
+ int aaMax = aa.annotations.length-1;\r
+\r
+ while( yPos < eRes )\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
+ if(av.hasHiddenColumns)\r
+ {\r
+ column = av.getColumnSelection().adjustForHiddenColumns(yPos);\r
+ if(column > aaMax)\r
+ {\r
+ break;\r
+ }\r
+ }\r
+ else\r
+ column = yPos;\r
\r
- }\r
+ yPos ++;\r
+\r
+ if (aa.annotations[column] == null)\r
+ {\r
+ x += av.charWidth;\r
+ continue;\r
+ }\r
\r
- if(row.isGraph && row.hasText)\r
- y+=av.charHeight;\r
- if(!row.isGraph)\r
- y+=aa[i].height;\r
+\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
+ else\r
+ g.fillRect(x, y1, av.charWidth, y2-y1 );\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
-\r
- // used by overview window\r
- public void drawGraph(Graphics g, AlignmentAnnotation aa,int width, int y)\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
+ // used by overview window\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 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) * y);\r
+ if(height>y)\r
+ height = y;\r
+\r
+ g.fillRect(x, y - height, av.charWidth, height);\r
+ x += av.charWidth;\r
+ }\r
}\r
- }\r
+\r
}\r
git://source.jalview.org / jalview.git / blobdiff