+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\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
+ * 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
+import javax.swing.*;\r
\r
-public class AnnotationPanel extends JPanel implements MouseListener, MouseMotionListener, ActionListener, AdjustmentListener\r
+import jalview.datamodel.*;\r
+\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\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
-\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
+ int activeRow = -1;\r
BufferedImage image;\r
+ BufferedImage fadedImage;\r
Graphics2D gg;\r
FontMetrics fm;\r
- int imgWidth=0;\r
-\r
+ int imgWidth = 0;\r
boolean fastPaint = false;\r
\r
- public static int GRAPH_HEIGHT = 40;\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
+ MAC = true;\r
+ }\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
- adjustPanelHeight();\r
-\r
+ ap.annotationScroller.getVerticalScrollBar().addAdjustmentListener(this);\r
+ }\r
\r
- ap.annotationScroller.getVerticalScrollBar().addAdjustmentListener( this );\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
+ ap.alabels.setScrollOffset( -evt.getValue());\r
}\r
\r
- public void adjustPanelHeight()\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
- if(aa!=null)\r
- for (int i = 0; i < aa.length; i++)\r
- {\r
- if(!aa[i].visible)\r
- continue;\r
\r
- aa[i].height = 0;\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
- if(aa[i].hasText)\r
- aa[i].height += av.charHeight;\r
- if (aa[i].hasIcons)\r
- aa[i].height += 16;\r
+ aa[i].height = 0;\r
\r
- if (aa[i].isGraph)\r
- aa[i].height += GRAPH_HEIGHT;\r
+ if (aa[i].hasText)\r
+ {\r
+ aa[i].height += av.charHeight;\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
+ if (aa[i].hasIcons)\r
+ {\r
+ aa[i].height += 16;\r
+ }\r
\r
- }\r
+ if (aa[i].graph > 0)\r
+ {\r
+ aa[i].height += aa[i].graphHeight;\r
+ }\r
\r
- public void addEditableColumn(int i)\r
- {\r
- if(activeRow==-1)\r
- {\r
- AlignmentAnnotation [] aa = av.alignment.getAlignmentAnnotation();\r
- for(int j=0; j<aa.length; j++)\r
- if(aa[j].editable)\r
+ if (aa[i].height == 0)\r
{\r
- activeRow = j;\r
- break;\r
+ aa[i].height = 20;\r
}\r
- }\r
\r
- if(activeRes==null)\r
+ height += aa[i].height;\r
+ }\r
+ }\r
+ else\r
{\r
- activeRes = new ArrayList();\r
- activeRes.add(String.valueOf(i));\r
- return;\r
+ height = 20;\r
}\r
\r
- activeRes.add(String.valueOf(i));\r
+ this.setPreferredSize(new Dimension(1, height));\r
\r
+ return height;\r
}\r
\r
-\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
- AlignmentAnnotation [] aa = av.alignment.getAlignmentAnnotation();\r
- Annotation [] anot = aa[activeRow].annotations;\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(evt.getActionCommand().equals(REMOVE))\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
+ 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
+ String label = JOptionPane.showInputDialog(this, "Enter Label ",\r
+ "Enter label",\r
+ JOptionPane.QUESTION_MESSAGE);\r
+\r
+ if (label == null)\r
+ {\r
+ return;\r
+ }\r
\r
- if(label.length()>0 && !aa[activeRow].hasText)\r
- aa[activeRow].hasText = true;\r
+ if ( (label.length() > 0) && !aa[activeRow].hasText)\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
- if(anot[index]==null)\r
- anot[index] = new Annotation(label, "", ' ',0);\r
+ int index = av.getColumnSelection().columnAt(i);\r
+\r
+ if(!av.colSel.isVisible(index))\r
+ continue;\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
+ else if (evt.getActionCommand().equals(COLOUR))\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
+ Color col = JColorChooser.showDialog(this,\r
+ "Choose foreground colour",\r
+ Color.black);\r
+\r
+ for (int i = 0; i < av.getColumnSelection().size(); i++)\r
+ {\r
+ int index = av.getColumnSelection().columnAt(i);\r
+\r
+ if(!av.colSel.isVisible(index))\r
+ continue;\r
+\r
+ if (anot[index] == null)\r
+ {\r
+ anot[index] = new Annotation("", "", ' ', 0);\r
+ }\r
+\r
+ anot[index].colour = col;\r
+ }\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
- type = 'E';\r
- symbol = "\u03B2";\r
- }\r
+ char type = 0;\r
+ String symbol = "\u03B1";\r
\r
- if(!aa[activeRow].hasIcons)\r
- aa[activeRow].hasIcons = true;\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?", symbol );\r
- if(label==null)\r
- label="";\r
+ String label = JOptionPane.showInputDialog(\r
+ "Enter a label for the structure?",\r
+ symbol);\r
\r
- if(label.length()>0 && !aa[activeRow].hasText)\r
- aa[activeRow].hasText = true;\r
+ if (label == null)\r
+ {\r
+ return;\r
+ }\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
+ if ( (label.length() > 0) && !aa[activeRow].hasText)\r
{\r
- anot[index] = new Annotation(label, "", type, 0);\r
+ aa[activeRow].hasText = true;\r
}\r
\r
- anot[ index ].secondaryStructure = type;\r
- anot[ index ].displayCharacter = label;\r
- }\r
+ for (int i = 0; i < av.getColumnSelection().size(); i++)\r
+ {\r
+ int index = av.getColumnSelection().columnAt(i);\r
+\r
+ if(!av.colSel.isVisible(index))\r
+ continue;\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
adjustPanelHeight();\r
- activeRes = null;\r
repaint();\r
- return;\r
-\r
\r
+ return;\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
public void mousePressed(MouseEvent evt)\r
{\r
- if (SwingUtilities.isRightMouseButton(evt))\r
+\r
+ AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
+ if (aa == null)\r
{\r
- if(activeRes==null)\r
+ return;\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 (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
+ if (SwingUtilities.isRightMouseButton(evt) && activeRow != -1)\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
pop.show(this, evt.getX(), evt.getY());\r
- return;\r
- }\r
-\r
\r
- AlignmentAnnotation [] aa = av.alignment.getAlignmentAnnotation();\r
- if(aa==null)\r
return;\r
+ }\r
\r
- int height = 0;\r
- activeRow = -1;\r
- for(int i=0; i<aa.length; i++)\r
+ if (aa == null)\r
{\r
- height+= aa[i].height;\r
+ return;\r
+ }\r
\r
- if(evt.getY()<height)\r
- {\r
- if(!aa[i].editable)\r
- {\r
- activeRes = null;\r
- continue;\r
- }\r
+ ap.scalePanel.mousePressed(evt);\r
\r
- activeRow = i;\r
- break;\r
- }\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
+ ap.scalePanel.mouseReleased(evt);\r
+ }\r
\r
- int res = evt.getX() / av.getCharWidth() + av.getStartRes();\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
+ public void mouseEntered(MouseEvent evt)\r
+ {\r
+ ap.scalePanel.mouseEntered(evt);\r
+ }\r
\r
- if(evt.isControlDown() || evt.isAltDown())\r
- addEditableColumn(res);\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
+ public void mouseExited(MouseEvent evt)\r
+ {\r
+ ap.scalePanel.mouseExited(evt);\r
+ }\r
\r
- else if(evt.isShiftDown())\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
+ public void mouseDragged(MouseEvent evt)\r
+ {\r
+ if (graphStretch > -1)\r
{\r
-\r
- if(activeRes==null)\r
- activeRes=new ArrayList();\r
- else\r
+ av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight +=\r
+ graphStretchY - evt.getY();\r
+ if (av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight < 0)\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
-\r
+ av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight = 0;\r
}\r
+ graphStretchY = evt.getY();\r
+ adjustPanelHeight();\r
+ ap.paintAlignment(true);\r
}\r
else\r
{\r
- activeRes = new ArrayList();\r
- activeRes.add( String.valueOf(res) );\r
+ ap.scalePanel.mouseDragged(evt);\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
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
public void mouseMoved(MouseEvent evt)\r
{\r
- ToolTipManager.sharedInstance().registerComponent(this);\r
- AlignmentAnnotation [] aa = av.alignment.getAlignmentAnnotation();\r
- if(aa==null)\r
+ AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
+\r
+ if (aa == null)\r
+ {\r
+ this.setToolTipText(null);\r
return;\r
+ }\r
\r
int row = -1;\r
- int height=0;\r
- for(int i=0; i<aa.length; i++)\r
- {\r
+ int height = 0;\r
\r
- if( aa[i].visible )\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
+ if (evt.getY() < height)\r
{\r
row = i;\r
+\r
break;\r
}\r
}\r
\r
- int res = evt.getX() / av.getCharWidth() + av.getStartRes();\r
- if(row>-1 && res<aa[row].annotations.length && aa[row].annotations[res]!=null)\r
+ if (row == -1)\r
{\r
- this.setToolTipText(aa[row].annotations[res].description);\r
- StringBuffer text = new StringBuffer("Sequence position " + (res + 1) +\r
- " " +\r
- aa[row].annotations[res].description);\r
- ap.alignFrame.statusBar.setText(text.toString());\r
+ this.setToolTipText(null);\r
+ return;\r
}\r
\r
+ int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();\r
\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
+ {\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
+ {\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] != null)\r
+ {\r
+ StringBuffer text = new StringBuffer("Sequence position " +\r
+ (res + 1));\r
+\r
+ if (aa[row].annotations[res].description != null)\r
+ {\r
+ text.append(" " + aa[row].annotations[res].description);\r
+ }\r
+\r
+ ap.alignFrame.statusBar.setText(text.toString());\r
+ }\r
+ }\r
+ else\r
+ {\r
+ this.setToolTipText(null);\r
+ }\r
}\r
- public void mouseClicked(MouseEvent evt) {}\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
+ g.fillRect(0, 0, getWidth(), getHeight());\r
\r
- if(fastPaint)\r
+ if (image != null)\r
{\r
- g.drawImage(image, 0, 0, this);\r
- fastPaint = false;\r
- return;\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
- imgWidth = (av.endRes-av.startRes+1) *av.charWidth;\r
-\r
- image = new BufferedImage(imgWidth,\r
- ap.annotationPanel.getHeight(),\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
- gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
- RenderingHints.VALUE_ANTIALIAS_ON);\r
- fm = gg.getFontMetrics();\r
- gg.setFont(av.getFont());\r
\r
- drawComponent( gg, av.startRes, av.endRes+1);\r
- g.drawImage( image, 0, 0, this);\r
+ if (av.antiAlias)\r
+ {\r
+ gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
+ RenderingHints.VALUE_ANTIALIAS_ON);\r
+ }\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
+ 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
- || av.alignment.getAlignmentAnnotation()==null\r
- || av.alignment.getAlignmentAnnotation().length<1\r
- )\r
{\r
- repaint();\r
- return;\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
\r
- gg.copyArea( 0,0, imgWidth, getHeight(), -horizontal*av.charWidth, 0 );\r
- int sr=av.startRes, er=av.endRes+1, transX=0;\r
+ gg.copyArea(0, 0, imgWidth, getHeight(), -horizontal * av.charWidth, 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
+ 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
\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
- repaint();\r
-}\r
+ fastPaint = true;\r
\r
+ repaint();\r
+\r
+ }\r
\r
- public void drawComponent(Graphics2D 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 (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
+\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
+ {\r
+ fadedImage = null;\r
+ }\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
+ g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight());\r
+\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.fillRect(0, 0, getWidth(), getHeight());\r
g.setColor(Color.black);\r
- g.drawString("Alignment has no annotations",20,15);\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
+ 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
+ int x = 0, y=0;\r
+ int column = 0;\r
+ char lastSS;\r
+ int lastSSX;\r
+ int iconOffset = 0;\r
boolean validRes = false;\r
- //\u03B2 \u03B1\r
\r
- for(int i=0; i<aa.length; i++)\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
- if(!row.visible)\r
+\r
+ if (!row.visible)\r
+ {\r
continue;\r
+ }\r
+\r
+ lastSS = ' ';\r
+ lastSSX = 0;\r
\r
- if(row.isGraph)\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
- if(row.hasText)\r
+\r
+ if (row.hasText)\r
+ {\r
+ iconOffset =av.charHeight -fm.getDescent();\r
y -= av.charHeight;\r
+ }\r
+ }\r
+ else if (row.hasText)\r
+ {\r
+ iconOffset = av.charHeight -fm.getDescent();\r
+\r
}\r
- if(row.hasText)\r
- iconOffset = av.charHeight/2;\r
else\r
+ {\r
iconOffset = 0;\r
+ }\r
\r
- for(j=startRes; j<endRes; j++)\r
+\r
+ if (av.updatingConsensus && aa[i] == av.consensus)\r
{\r
- validRes = row.annotations[j]==null?false:true;\r
+ y += av.charHeight;\r
\r
- x = (j-startRes)*av.charWidth;\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
- if(activeRow==i)\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.red);\r
+ g.setColor(Color.black);\r
+ // g.drawString("Calculating Conservation.....",20, y-row.height/2);\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
+ 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
+\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
+ if ( (row.annotations.length <= column) ||\r
+ (row.annotations[column] == null))\r
+ {\r
+ validRes = false;\r
+ }\r
+ else\r
+ {\r
+ validRes = true;\r
+ }\r
\r
+ if (activeRow == i)\r
+ {\r
+ g.setColor(Color.red);\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
+ if (av.getColumnSelection() != null)\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
+ 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
- else if( (row.annotations[j].secondaryStructure=='H'\r
- || row.annotations[j].secondaryStructure=='E') &&\r
- (row.annotations[j-1]==null ||\r
- row.annotations[j].secondaryStructure!=row.annotations[j-1].secondaryStructure))\r
-\r
- g.drawString(row.annotations[j].displayCharacter, x, y + iconOffset + 2);\r
-\r
- if(!row.hasIcons)\r
- g.drawString(row.annotations[j].displayCharacter, x + charOffset,\r
- y + iconOffset + 2);\r
- }\r
-\r
- if(row.hasIcons)\r
- if(!validRes || row.annotations[j].secondaryStructure!=lastSS[i])\r
- {\r
- switch (lastSS[i])\r
- {\r
- case 'H':\r
- g.setColor(HELIX_COLOUR);\r
- g.fillRoundRect(lastSSX[i], y+4 + iconOffset, x-lastSSX[i], 7, 8, 8);\r
- break;\r
- case 'E':\r
- g.setColor(SHEET_COLOUR);\r
- g.fillRect(lastSSX[i], y + 4 + iconOffset, x-lastSSX[i]-4, 7);\r
- g.fillPolygon(new int[] {x - 4, x- 4, x }\r
- , new int[]{y+ iconOffset, y + 14+ iconOffset, y + 8+ iconOffset}, 3);\r
- break;\r
- case 'C':\r
- break;\r
- default :\r
- g.setColor(Color.gray);\r
- g.fillRect(lastSSX[i], y+6+ iconOffset, x-lastSSX[i], 2);\r
- break;\r
- }\r
-\r
- if(validRes)\r
- lastSS[i] = row.annotations[j].secondaryStructure;\r
+ }\r
+\r
+ if (av.validCharWidth && validRes\r
+ && row.annotations[column].displayCharacter != null\r
+ && (row.annotations[column].displayCharacter.length() > 0))\r
+ {\r
+\r
+ int charOffset = (av.charWidth -\r
+ fm.charWidth(row.annotations[column].\r
+ displayCharacter.charAt(\r
+ 0))) / 2;\r
+\r
+ if (row.annotations[column].colour == null)\r
+ g.setColor(Color.black);\r
else\r
- lastSS[i] = ' ';\r
- lastSSX[i] = x;\r
- }\r
+ g.setColor(row.annotations[column].colour);\r
\r
- if (validRes && row.isGraph)\r
- {\r
- g.setColor(new Color(0,0,180));\r
- int height = (int)((row.annotations[j].value / row.graphMax)*GRAPH_HEIGHT);\r
+ 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
- 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
+ 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,\r
+ 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[]\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
+ 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
+ if (validRes)\r
+ {\r
+ lastSS = row.annotations[column].secondaryStructure;\r
+ }\r
+ else\r
+ {\r
+ lastSS = ' ';\r
+ }\r
+\r
+ lastSSX = (x * av.charWidth);\r
+ }\r
+ }\r
\r
- total += row.annotations[i2].value;\r
- }\r
+ column++;\r
+ x++;\r
+ }\r
\r
- total/=row.windowLength;\r
- height = (int)( (total / row.graphMax) *GRAPH_HEIGHT);\r
+ if (column >= row.annotations.length)\r
+ {\r
+ column = row.annotations.length - 1;\r
+ }\r
\r
- }\r
- g.setColor(row.annotations[j].colour);\r
- g.fillRect(x, y-height, av.charWidth, height );\r
- }\r
+ // x ++;\r
\r
+ if (row.hasIcons)\r
+ {\r
+ switch (lastSS)\r
+ {\r
+ case 'H':\r
+ g.setColor(HELIX_COLOUR);\r
+ if (MAC)\r
+ {\r
+ //Off by 1 offset when drawing rects and ovals\r
+ //to offscreen image on the MAC\r
+ g.fillRoundRect(lastSSX, y + 4 + iconOffset,\r
+ (x * av.charWidth) - lastSSX, 7, 8, 8);\r
+ break;\r
+ }\r
+\r
+ int sCol = (lastSSX / av.charWidth) + startRes;\r
+ int x1 = lastSSX;\r
+ int x2 = (x * av.charWidth);\r
+\r
+ if (sCol == 0 ||\r
+ row.annotations[sCol - 1] == null ||\r
+ row.annotations[sCol - 1].secondaryStructure != 'H')\r
+ {\r
+ g.fillArc(lastSSX, y + 4 + iconOffset, av.charWidth, 8, 90, 180);\r
+ x1 += av.charWidth / 2;\r
+ }\r
+\r
+ if (row.annotations[column] == null ||\r
+ row.annotations[column].secondaryStructure != 'H')\r
+ {\r
+ g.fillArc( (x * av.charWidth) - av.charWidth,\r
+ y + 4 + iconOffset, av.charWidth, 8, 270,\r
+ 180);\r
+ x2 -= av.charWidth / 2;\r
+ }\r
+\r
+ g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);\r
+\r
+ break;\r
+\r
+ case 'E':\r
+ g.setColor(SHEET_COLOUR);\r
+\r
+ if (row.annotations[endRes] == null\r
+ || row.annotations[endRes].secondaryStructure != 'E')\r
+ {\r
+ g.fillRect(lastSSX, y + 4 + iconOffset,\r
+ (x * av.charWidth) - lastSSX - 4, 7);\r
+ g.fillPolygon(new int[]\r
+ { (x * av.charWidth) - 4,\r
+ (x * av.charWidth) - 4,\r
+ (x * av.charWidth)},\r
+ new int[]\r
+ {\r
+ y + iconOffset, y + 14 + iconOffset,\r
+ y + 7 + iconOffset\r
+ }, 3);\r
+ }\r
+ else\r
+ {\r
+ g.fillRect(lastSSX, y + 4 + iconOffset,\r
+ (x + 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
+ 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
+ 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
+ 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
+ {\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
- x+=av.charWidth;\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
+ if (sRes > aa.annotations.length)\r
+ {\r
+ return;\r
+ }\r
+\r
+ int x = 0;\r
+\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
+\r
+ if (sRes == 0)\r
+ {\r
+ x++;\r
+ }\r
+\r
+ int y1 = y, y2 = y;\r
+ float range = max - min;\r
+\r
+ ////Draw origin\r
+ if (min < 0)\r
+ {\r
+ y2 = y - (int) ( (0 - min / range) * graphHeight);\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
- if(row.hasIcons)\r
- switch (lastSS[i])\r
+ int column;\r
+ int aaMax = aa.annotations.length - 1;\r
+\r
+ while (x < eRes - sRes)\r
+ {\r
+ column = sRes + x;\r
+ if (av.hasHiddenColumns)\r
{\r
- 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
+ column = av.getColumnSelection().adjustForHiddenColumns(column);\r
+ }\r
\r
+ if (column > aaMax)\r
+ {\r
+ break;\r
}\r
\r
- if(row.isGraph && row.hasText)\r
- y+=av.charHeight;\r
- if(!row.isGraph)\r
- y+=aa[i].height;\r
+ if (aa.annotations[column] == null || aa.annotations[column - 1] == null)\r
+ {\r
+ x++;\r
+ continue;\r
+ }\r
+\r
+ if (aa.annotations[column].colour == null)\r
+ g.setColor(Color.black);\r
+ else\r
+ g.setColor(aa.annotations[column].colour);\r
+\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
+ 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[]\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
+\r
+ int x = 0, y1 = y, y2 = y;\r
+\r
+ float range = max - min;\r
+\r
+ if (min < 0)\r
+ {\r
+ y2 = y - (int) ( (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
+ int column;\r
+ int aaMax = aa.annotations.length - 1;\r
+\r
+ while (x < eRes - sRes)\r
+ {\r
+ column = sRes + x;\r
+ if (av.hasHiddenColumns)\r
+ {\r
+ column = av.getColumnSelection().adjustForHiddenColumns(column);\r
+ }\r
+\r
+ if (column > aaMax)\r
+ {\r
+ break;\r
+ }\r
+\r
+ if (aa.annotations[column] == null)\r
+ {\r
+ x++;\r
+ continue;\r
+ }\r
+\r
+ if (aa.annotations[column].colour == null)\r
+ g.setColor(Color.black);\r
+ else\r
+ g.setColor(aa.annotations[column].colour);\r
+\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
+ else\r
+ {\r
+ g.fillRect(x * av.charWidth, y1, av.charWidth, y2 - y1);\r
+ }\r
+\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[]\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
// used by overview window\r
- public void drawGraph(Graphics g, AlignmentAnnotation aa,int width, int y)\r
+ public void drawGraph(Graphics g, AlignmentAnnotation aa, int width, int y,\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
- int x = 0;\r
- for(int j=0; j<aa.annotations.length; j++)\r
+ g.fillRect(0, 0, width, y);\r
+ g.setColor(new Color(0, 0, 180));\r
+\r
+ int x = 0, height;\r
+\r
+ for (int j = sRes; j < eRes; j++)\r
{\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
+ if (aa.annotations[j] != null)\r
+ {\r
+ if (aa.annotations[j].colour == null)\r
+ g.setColor(Color.black);\r
+ else\r
+ g.setColor(aa.annotations[j].colour);\r
+\r
+ height = (int) ( (aa.annotations[j].value / aa.graphMax) * y);\r
+ if (height > y)\r
+ {\r
+ height = y;\r
+ }\r
+\r
+ g.fillRect(x, y - height, av.charWidth, height);\r
+ }\r
+ x += av.charWidth;\r
}\r
}\r
+\r
}\r