+/*\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
+import java.util.*;\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
-{\r
- AlignViewport av;\r
- AlignmentPanel ap;\r
- int activeRow =-1;\r
+import jalview.datamodel.*;\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
+public class AnnotationPanel\r
+ extends JPanel implements MouseListener,\r
+ MouseMotionListener, ActionListener, AdjustmentListener\r
+{\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
+ public static int GRAPH_HEIGHT = 40;\r
+ AlignViewport av;\r
+ AlignmentPanel ap;\r
+ int activeRow = -1;\r
+ ArrayList activeRes;\r
BufferedImage image;\r
Graphics2D gg;\r
FontMetrics fm;\r
- int imgWidth=0;\r
-\r
-\r
-\r
+ int imgWidth = 0;\r
+ boolean fastPaint = false;\r
\r
public AnnotationPanel(AlignmentPanel ap)\r
{\r
addMouseMotionListener(this);\r
adjustPanelHeight();\r
\r
-\r
- ap.annotationScroller.getVerticalScrollBar().addAdjustmentListener( this );\r
+ ap.annotationScroller.getVerticalScrollBar().addAdjustmentListener(this);\r
}\r
\r
public void adjustmentValueChanged(AdjustmentEvent evt)\r
{\r
- ap.alabels.setScrollOffset( -evt.getValue() );\r
+ ap.alabels.setScrollOffset( -evt.getValue());\r
}\r
\r
public void adjustPanelHeight()\r
// 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 != null)\r
{\r
- if(!aa[i].visible)\r
- continue;\r
+ for (int i = 0; i < aa.length; i++)\r
+ {\r
+ if (!aa[i].visible)\r
+ {\r
+ continue;\r
+ }\r
\r
- aa[i].height = 0;\r
+ aa[i].height = 0;\r
\r
- if(aa[i].hasText)\r
- aa[i].height += av.charHeight;\r
- if (aa[i].hasIcons)\r
- aa[i].height += 16;\r
+ if (aa[i].hasText)\r
+ {\r
+ aa[i].height += av.charHeight;\r
+ }\r
\r
- if (aa[i].isGraph)\r
- aa[i].height += 50;\r
+ if (aa[i].hasIcons)\r
+ {\r
+ aa[i].height += 16;\r
+ }\r
\r
- if(aa[i].height==0)\r
- aa[i].height = 20;\r
- height += aa[i].height;\r
+ if (aa[i].isGraph)\r
+ {\r
+ aa[i].height += GRAPH_HEIGHT;\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
- else height=20;\r
- this.setPreferredSize(new Dimension(1, height));\r
\r
+ this.setPreferredSize(new Dimension(1, height));\r
}\r
\r
public void addEditableColumn(int i)\r
{\r
- if(activeRow==-1)\r
+ if (activeRow == -1)\r
{\r
- AlignmentAnnotation [] aa = av.alignment.getAlignmentAnnotation();\r
- for(int j=0; j<aa.length; j++)\r
- if(aa[j].editable)\r
+ AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
+\r
+ for (int j = 0; j < aa.length; j++)\r
+ {\r
+ if (aa[j].editable)\r
{\r
activeRow = j;\r
+\r
break;\r
}\r
+ }\r
}\r
\r
- if(activeRes==null)\r
+ if (activeRes == null)\r
{\r
activeRes = new ArrayList();\r
activeRes.add(String.valueOf(i));\r
+\r
return;\r
}\r
\r
activeRes.add(String.valueOf(i));\r
-\r
}\r
\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
-\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 < 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
+ 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
+ String label = JOptionPane.showInputDialog(this, "Enter Label ",\r
+ "Enter label",\r
+ JOptionPane.QUESTION_MESSAGE);\r
+\r
+ if (label == null)\r
+ {\r
label = "";\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 < 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
+\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 < activeRes.size(); i++)\r
+ {\r
+ int index = Integer.parseInt(activeRes.get(i).toString());\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
+ label = "";\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 < activeRes.size(); i++)\r
+ {\r
+ int index = Integer.parseInt(activeRes.get(i).toString());\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
public void mousePressed(MouseEvent evt)\r
{\r
if (SwingUtilities.isRightMouseButton(evt))\r
{\r
- if(activeRes==null)\r
+ if (activeRes == 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
+\r
return;\r
}\r
\r
+ AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
\r
- AlignmentAnnotation [] aa = av.alignment.getAlignmentAnnotation();\r
- if(aa==null)\r
+ if (aa == null)\r
+ {\r
return;\r
+ }\r
\r
int height = 0;\r
activeRow = -1;\r
- for(int i=0; i<aa.length; i++)\r
+\r
+ for (int i = 0; i < aa.length; i++)\r
{\r
- height+= aa[i].height;\r
+ height += aa[i].height;\r
\r
- if(evt.getY()<height)\r
+ if (evt.getY() < height)\r
{\r
- if(!aa[i].editable)\r
+ if (!aa[i].editable)\r
{\r
activeRes = null;\r
+\r
continue;\r
}\r
\r
activeRow = i;\r
+\r
break;\r
}\r
}\r
\r
+ int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();\r
\r
- int res = evt.getX() / av.getCharWidth() + av.getStartRes();\r
-\r
- if(evt.isControlDown() || evt.isAltDown())\r
+ if (evt.isControlDown() || evt.isAltDown())\r
+ {\r
addEditableColumn(res);\r
-\r
- else if(evt.isShiftDown())\r
+ }\r
+ else if (evt.isShiftDown())\r
{\r
-\r
- if(activeRes==null)\r
- activeRes=new ArrayList();\r
+ if (activeRes == null)\r
+ {\r
+ activeRes = new ArrayList();\r
+ }\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
+ int start = Integer.parseInt(activeRes.get(activeRes.size() -\r
+ 1).toString());\r
+ int end = res;\r
+\r
+ if (end < start)\r
+ {\r
+ int temp = end;\r
+ end = start;\r
+ start = temp;\r
+ }\r
\r
+ for (int n = start; n <= end; n++)\r
+ {\r
+ addEditableColumn(n);\r
+ }\r
}\r
}\r
else\r
{\r
- activeRes = new ArrayList();\r
- activeRes.add( String.valueOf(res) );\r
+ activeRes = new ArrayList();\r
+ activeRes.add(String.valueOf(res));\r
}\r
\r
repaint();\r
-\r
}\r
+\r
public void mouseReleased(MouseEvent evt)\r
- { }\r
+ {\r
+ }\r
+\r
public void mouseEntered(MouseEvent evt)\r
- { }\r
+ {\r
+ }\r
+\r
public void mouseExited(MouseEvent evt)\r
- { }\r
+ {\r
+ }\r
+\r
public void mouseDragged(MouseEvent evt)\r
- { }\r
+ {\r
+ }\r
+\r
public void mouseMoved(MouseEvent evt)\r
{\r
ToolTipManager.sharedInstance().registerComponent(this);\r
- AlignmentAnnotation [] aa = av.alignment.getAlignmentAnnotation();\r
- if(aa==null)\r
+\r
+ AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
+\r
+ if (aa == null)\r
+ {\r
return;\r
+ }\r
\r
int row = -1;\r
- int height=0;\r
- for(int i=0; i<aa.length; i++)\r
- {\r
+ int 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 && aa[row].annotations[res]!=null)\r
+ int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();\r
+\r
+ if ( (row > -1) && (res < aa[row].annotations.length) &&\r
+ (aa[row].annotations[res] != null))\r
+ {\r
this.setToolTipText(aa[row].annotations[res].description);\r
\r
+ StringBuffer text = new StringBuffer("Sequence position " +\r
+ (res + 1) + " " +\r
+ aa[row].annotations[res].description);\r
+ ap.alignFrame.statusBar.setText(text.toString());\r
+ }\r
}\r
- public void mouseClicked(MouseEvent evt) {}\r
\r
+ public void mouseClicked(MouseEvent evt)\r
+ {\r
+ }\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
- imgWidth = (av.endRes-av.startRes+1) *av.charWidth;\r
+ if (fastPaint)\r
+ {\r
+ g.drawImage(image, 0, 0, this);\r
+ fastPaint = false;\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
+ return;\r
+ }\r
\r
+ imgWidth = (av.endRes - av.startRes + 1) * av.charWidth;\r
\r
- drawComponent( gg, av.startRes, av.endRes+1);\r
- g.drawImage( image, 0, 0, this);\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
+\r
+ gg.setFont(av.getFont());\r
+ fm = gg.getFontMetrics();\r
+\r
+ drawComponent(gg, av.startRes, av.endRes + 1);\r
+ g.drawImage(image, 0, 0, this);\r
}\r
\r
public void fastPaint(int horizontal)\r
-{\r
- if(image==null || horizontal ==0)\r
{\r
- repaint();\r
- return;\r
- }\r
+ if ( (horizontal == 0) ||\r
+ (av.alignment.getAlignmentAnnotation() == null) ||\r
+ (av.alignment.getAlignmentAnnotation().length < 1))\r
+ {\r
+ repaint();\r
\r
- gg.copyArea( 0,0, imgWidth, getHeight(), -horizontal*av.charWidth, 0 );\r
- int sr=av.startRes, er=av.endRes+1, transX=0;\r
+ return;\r
+ }\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
+ 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
- gg.translate(transX, 0);\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
- drawComponent(gg, sr, er);\r
+ gg.translate(transX, 0);\r
\r
- gg.translate( -transX, 0 );\r
+ drawComponent(gg, sr, er);\r
\r
- getGraphics().drawImage(image, 0, 0, this);\r
-}\r
+ gg.translate( -transX, 0);\r
\r
+ fastPaint = true;\r
+ repaint();\r
+ }\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
+ g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight());\r
+\r
+ if ( (av.alignment.getAlignmentAnnotation() == null) ||\r
+ (av.alignment.getAlignmentAnnotation().length < 1))\r
{\r
+ g.setColor(Color.white);\r
+ g.fillRect(0, 0, getWidth(), getHeight());\r
g.setColor(Color.black);\r
- g.drawString("Alignment has no annotations",20,15);\r
+ g.drawString("Alignment has no annotations", 20, 15);\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 j;\r
+ int x = 0;\r
+ int y = 0;\r
+ char[] lastSS = new char[aa.length];\r
+ int[] lastSSX = new int[aa.length];\r
+ int iconOffset = av.charHeight / 2;\r
boolean validRes = false;\r
+\r
//\u03B2 \u03B1\r
- for(int i=0; i<aa.length; i++)\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
- if(row.isGraph)\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
+\r
+ if (row.hasText)\r
+ {\r
y -= av.charHeight;\r
+ }\r
+ }\r
+\r
+ if (row.hasText)\r
+ {\r
+ iconOffset = av.charHeight / 2;\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
+ for (j = startRes; j < endRes; j++)\r
{\r
- validRes = row.annotations[j]==null?false:true;\r
-\r
- x = (j-startRes)*av.charWidth;\r
+ if ( (row.annotations.length <= j) ||\r
+ (row.annotations[j] == null))\r
+ {\r
+ validRes = false;\r
+ }\r
+ else\r
+ {\r
+ validRes = true;\r
+ }\r
\r
+ x = (j - startRes) * av.charWidth;\r
\r
- if(activeRow==i)\r
- {\r
+ if (activeRow == i)\r
+ {\r
+ g.setColor(Color.red);\r
\r
- g.setColor(Color.red);\r
+ if (activeRes != null)\r
+ {\r
+ for (int n = 0; n < activeRes.size(); n++)\r
+ {\r
+ int v = Integer.parseInt(activeRes.get(n).toString());\r
+\r
+ if (v == j)\r
+ {\r
+ g.fillRect( (j - startRes) * av.charWidth, y,\r
+ av.charWidth, row.height);\r
+ }\r
+ }\r
+ }\r
+ }\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
+ if (validRes &&\r
+ (row.annotations[j].displayCharacter.length() > 0))\r
+ {\r
+ int charOffset = (av.charWidth -\r
+ fm.charWidth(row.annotations[j].displayCharacter.\r
+ charAt(\r
+ 0))) / 2;\r
+ g.setColor(row.annotations[j].colour);\r
\r
+ if (j == 0)\r
+ {\r
+ if ( (row.annotations[0].secondaryStructure == 'H') ||\r
+ (row.annotations[0].secondaryStructure == 'E'))\r
+ {\r
+ g.drawString(row.annotations[j].displayCharacter,\r
+ x, y + iconOffset + 2);\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 -\r
+ 1].secondaryStructure)))\r
+ {\r
+ g.drawString(row.annotations[j].displayCharacter, x,\r
+ y + iconOffset + 2);\r
+ }\r
\r
+ if (!row.hasIcons)\r
+ {\r
+ g.drawString(row.annotations[j].displayCharacter,\r
+ x + charOffset, y + iconOffset + 2);\r
+ }\r
+ }\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 (row.hasIcons)\r
+ {\r
+ if (!validRes ||\r
+ (row.annotations[j].secondaryStructure != lastSS[i]))\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
+ switch (lastSS[i])\r
+ {\r
+ case 'H':\r
+ g.setColor(HELIX_COLOUR);\r
+ g.fillRoundRect(lastSSX[i], y + 4 + iconOffset,\r
+ x - lastSSX[i], 7, 8, 8);\r
+\r
+ break;\r
+\r
+ case 'E':\r
+ g.setColor(SHEET_COLOUR);\r
+ g.fillRect(lastSSX[i], y + 4 + iconOffset,\r
+ x - lastSSX[i] - 4, 7);\r
+ g.fillPolygon(new int[]\r
+ {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
+ case 'C':\r
+ break;\r
+\r
+ default:\r
+ g.setColor(Color.gray);\r
+ g.fillRect(lastSSX[i], y + 6 + iconOffset,\r
+ x - lastSSX[i], 2);\r
+\r
+ break;\r
+ }\r
+\r
+ if (validRes)\r
+ {\r
+ lastSS[i] = row.annotations[j].secondaryStructure;\r
+ }\r
+ else\r
+ {\r
+ lastSS[i] = ' ';\r
+ }\r
+\r
+ lastSSX[i] = x;\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
\r
- g.drawString(row.annotations[j].displayCharacter, x, y + iconOffset + 2);\r
+ if (validRes && row.isGraph)\r
+ {\r
+ g.setColor(new Color(0, 0, 180));\r
\r
- if(!row.hasIcons)\r
- g.drawString(row.annotations[j].displayCharacter, x + charOffset,\r
- y + iconOffset + 2);\r
- }\r
-\r
- if(row.hasIcons)\r
- if(!validRes || row.annotations[j].secondaryStructure!=lastSS[i])\r
- {\r
- switch (lastSS[i])\r
- {\r
- case 'H':\r
- g.setColor(HELIX_COLOUR);\r
- g.fillRoundRect(lastSSX[i], y+4 + iconOffset, x-lastSSX[i], 7, 8, 8);\r
- break;\r
- case 'E':\r
- g.setColor(SHEET_COLOUR);\r
- g.fillRect(lastSSX[i], y + 4 + iconOffset, x-lastSSX[i]-4, 7);\r
- g.fillPolygon(new int[] {x - 4, x- 4, x }\r
- , new int[]{y+ iconOffset, y + 14+ iconOffset, y + 8+ iconOffset}, 3);\r
- break;\r
- case 'C':\r
- break;\r
- default :\r
- g.setColor(Color.gray);\r
- g.fillRect(lastSSX[i], y+6+ iconOffset, x-lastSSX[i], 2);\r
- break;\r
- }\r
-\r
- if(validRes)\r
- lastSS[i] = row.annotations[j].secondaryStructure;\r
- else\r
- lastSS[i] = ' ';\r
- lastSSX[i] = x;\r
- }\r
-\r
- if (validRes && row.isGraph)\r
- {\r
- g.setColor(new Color(0,0,180));\r
- int height = (int)((row.annotations[j].value / row.graphMax)*50);\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
-\r
- total += row.annotations[i2].value;\r
- }\r
-\r
- total/=row.windowLength;\r
- height = (int)( (total / row.graphMax) *50);\r
-\r
- }\r
-\r
- g.fillRect(x, y-height, av.charWidth, height );\r
- }\r
+ int height = (int) ( (row.annotations[j].value / row.graphMax) *\r
+ GRAPH_HEIGHT);\r
+\r
+ if (row.windowLength > 1)\r
+ {\r
+ int total = 0;\r
\r
+ for (int i2 = j - (row.windowLength / 2);\r
+ i2 < (j + (row.windowLength / 2)); i2++)\r
+ {\r
+ if ( (i2 < 0) || (i2 >= av.alignment.getWidth()))\r
+ {\r
+ continue;\r
+ }\r
+\r
+ total += row.annotations[i2].value;\r
+ }\r
+\r
+ total /= row.windowLength;\r
+ height = (int) ( (total / row.graphMax) * GRAPH_HEIGHT);\r
+ }\r
\r
+ g.setColor(row.annotations[j].colour);\r
+ g.fillRect(x, y - height, av.charWidth, height);\r
+ }\r
}\r
\r
- x+=av.charWidth;\r
+ x += av.charWidth;\r
\r
- if(row.hasIcons)\r
- switch (lastSS[i])\r
+ if (row.hasIcons)\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
+ switch (lastSS[i])\r
+ {\r
+ case 'H':\r
+ g.setColor(HELIX_COLOUR);\r
+ g.fillRoundRect(lastSSX[i], y + 4 + iconOffset,\r
+ x - lastSSX[i], 7, 8, 8);\r
+\r
+ break;\r
+\r
+ case 'E':\r
+ g.setColor(SHEET_COLOUR);\r
+ g.fillRect(lastSSX[i], y + 4 + iconOffset,\r
+ x - lastSSX[i] - 4, 7);\r
+ g.fillPolygon(new int[]\r
+ {x - 4, x - 4, x},\r
+ new int[]\r
+ {\r
+ y + iconOffset, y + 14 + iconOffset,\r
+ y + 7 + iconOffset\r
+ }, 3);\r
+\r
+ break;\r
+\r
+ case 'C':\r
+ break;\r
+\r
+ default:\r
+ g.setColor(Color.gray);\r
+ g.fillRect(lastSSX[i], y + 6 + iconOffset, x - lastSSX[i], 2);\r
+\r
+ break;\r
+ }\r
+ }\r
\r
+ if (row.isGraph && row.hasText)\r
+ {\r
+ y += av.charHeight;\r
}\r
\r
- if(row.isGraph && row.hasText)\r
- y+=av.charHeight;\r
- if(!row.isGraph)\r
- y+=aa[i].height;\r
+ if (!row.isGraph)\r
+ {\r
+ y += aa[i].height;\r
+ }\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
{\r
g.setColor(Color.white);\r
- g.fillRect(0,0,width, y);\r
- g.setColor(new Color(0,0,180));\r
+ g.fillRect(0, 0, width, y);\r
+ g.setColor(new Color(0, 0, 180));\r
+\r
int x = 0;\r
- for(int j=0; j<aa.annotations.length; j++)\r
+\r
+ for (int j = 0; j < aa.annotations.length; j++)\r
{\r
g.setColor(new Color(0, 0, 180));\r
- int height = (int) ( (aa.annotations[j].value / aa.graphMax) * 50);\r
+\r
+ int height = (int) ( (aa.annotations[j].value / aa.graphMax) *\r
+ GRAPH_HEIGHT);\r
g.fillRect(x, y - height, av.charWidth, height);\r
- x+=av.charWidth;\r
+ x += av.charWidth;\r
}\r
}\r
}\r
git://source.jalview.org / jalview.git / blobdiff