/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
*\r
* This program is free software; you can redistribute it and/or\r
* modify it under the terms of the GNU General Public License\r
*/\r
package jalview.gui;\r
\r
-import java.util.*;\r
-\r
import java.awt.*;\r
import java.awt.event.*;\r
import java.awt.image.*;\r
\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
- 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
- public static int GRAPH_HEIGHT = 40;\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
- Vector activeRes;\r
BufferedImage image;\r
+ BufferedImage fadedImage;\r
Graphics2D gg;\r
FontMetrics fm;\r
int imgWidth = 0;\r
boolean fastPaint = false;\r
\r
+ //Used For mouse Dragging and resizing graphs\r
+ int graphStretch = -1;\r
+ int graphStretchY = -1;\r
+ int min; //used by mouseDragged to see if user\r
+ int max; //used by mouseDragged to see if user\r
+ boolean mouseDragging = false;\r
+\r
+ boolean MAC = false;\r
+\r
+ /**\r
+ * Creates a new AnnotationPanel object.\r
+ *\r
+ * @param ap DOCUMENT ME!\r
+ */\r
public AnnotationPanel(AlignmentPanel ap)\r
{\r
+\r
+ if (System.getProperty("os.name").startsWith("Mac"))\r
+ {\r
+ MAC = true;\r
+ }\r
+\r
ToolTipManager.sharedInstance().registerComponent(this);\r
ToolTipManager.sharedInstance().setInitialDelay(0);\r
ToolTipManager.sharedInstance().setDismissDelay(10000);\r
ap.annotationScroller.getVerticalScrollBar().addAdjustmentListener(this);\r
}\r
\r
+ public AnnotationPanel(AlignViewport av)\r
+ {\r
+ this.av = av;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
public void adjustmentValueChanged(AdjustmentEvent evt)\r
{\r
ap.alabels.setScrollOffset( -evt.getValue());\r
}\r
\r
- public void adjustPanelHeight()\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
+ public int adjustPanelHeight()\r
{\r
// setHeight of panels\r
AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
aa[i].height += 16;\r
}\r
\r
- if (aa[i].isGraph)\r
+ if (aa[i].graph > 0)\r
{\r
- aa[i].height += GRAPH_HEIGHT;\r
+ aa[i].height += aa[i].graphHeight;\r
}\r
\r
if (aa[i].height == 0)\r
}\r
\r
this.setPreferredSize(new Dimension(1, height));\r
- }\r
-\r
-\r
- public void removeEditableColumn(int col)\r
- {\r
- if (activeRow == -1)\r
- {\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
- break;\r
- }\r
- }\r
- }\r
\r
- if (activeRes != null && activeRes.contains(String.valueOf(col)))\r
- {\r
- activeRes.removeElement(String.valueOf(col));\r
- }\r
- repaint();\r
- }\r
-\r
-\r
- public void addEditableColumn(int col)\r
- {\r
- if (activeRow == -1)\r
- {\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
- break;\r
- }\r
- }\r
- }\r
-\r
- if (activeRes == null)\r
- activeRes = new Vector();\r
-\r
- if (!activeRes.contains(String.valueOf(col)))\r
- activeRes.addElement(String.valueOf(col));\r
-\r
- repaint();\r
+ return height;\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
+ 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
{\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
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 < activeRes.size(); i++)\r
+ for (int i = 0; i < av.getColumnSelection().size(); i++)\r
{\r
- int index = Integer.parseInt(activeRes.get(i).toString());\r
+ int index = av.getColumnSelection().columnAt(i);\r
+\r
+ if(!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
"Choose foreground colour",\r
Color.black);\r
\r
- for (int i = 0; i < activeRes.size(); i++)\r
+ for (int i = 0; i < av.getColumnSelection().size(); i++)\r
{\r
- int index = Integer.parseInt(activeRes.get(i).toString());\r
+ int index = av.getColumnSelection().columnAt(i);\r
+\r
+ if(!av.colSel.isVisible(index))\r
+ continue;\r
\r
if (anot[index] == null)\r
{\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 < activeRes.size(); i++)\r
+ for (int i = 0; i < av.getColumnSelection().size(); i++)\r
{\r
- int index = Integer.parseInt(activeRes.get(i).toString());\r
+ int index = av.getColumnSelection().columnAt(i);\r
+\r
+ if(!av.colSel.isVisible(index))\r
+ continue;\r
\r
if (anot[index] == null)\r
{\r
}\r
\r
adjustPanelHeight();\r
- activeRes = null;\r
repaint();\r
\r
return;\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
public void mousePressed(MouseEvent evt)\r
{\r
+\r
+ AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
+ if (aa == null)\r
+ {\r
+ return;\r
+ }\r
+\r
int height = 0;\r
activeRow = -1;\r
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
\r
for (int i = 0; i < aa.length; i++)\r
{\r
- height += aa[i].height;\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
- activeRow = i;\r
- else\r
- activeRes = null;\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 (SwingUtilities.isRightMouseButton(evt))\r
+ if (SwingUtilities.isRightMouseButton(evt) && activeRow != -1)\r
{\r
- if (activeRes == null)\r
+ if (av.getColumnSelection() == null)\r
{\r
return;\r
}\r
\r
-\r
JPopupMenu pop = new JPopupMenu("Structure type");\r
JMenuItem item = new JMenuItem(HELIX);\r
item.addActionListener(this);\r
return;\r
}\r
\r
-\r
if (aa == null)\r
{\r
return;\r
}\r
\r
+ ap.scalePanel.mousePressed(evt);\r
\r
- int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();\r
-\r
- if (evt.isControlDown() || evt.isAltDown())\r
- {\r
- addEditableColumn(res);\r
- }\r
- else if (evt.isShiftDown())\r
- {\r
- if (activeRes == null)\r
- {\r
- activeRes = new Vector();\r
- }\r
- else\r
- {\r
- int start = Integer.parseInt(activeRes.get(activeRes.size() -\r
- 1).toString());\r
- int end = res;\r
-\r
- if (end < start)\r
- {\r
- int temp = end;\r
- end = start;\r
- start = temp;\r
- }\r
-\r
- for (int n = start; n <= end; n++)\r
- {\r
- addEditableColumn(n);\r
- }\r
- }\r
- }\r
- else\r
- {\r
- activeRes = new Vector();\r
- activeRes.addElement(String.valueOf(res));\r
- }\r
-\r
- repaint();\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
+ /**\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
+ /**\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
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
public void mouseDragged(MouseEvent evt)\r
{\r
+ if (graphStretch > -1)\r
+ {\r
+ av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight +=\r
+ graphStretchY - evt.getY();\r
+ if (av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight < 0)\r
+ {\r
+ av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight = 0;\r
+ }\r
+ graphStretchY = evt.getY();\r
+ adjustPanelHeight();\r
+ ap.paintAlignment(true);\r
+ }\r
+ else\r
+ {\r
+ ap.scalePanel.mouseDragged(evt);\r
+ }\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
public void mouseMoved(MouseEvent evt)\r
{\r
AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
\r
if (aa == null)\r
{\r
+ this.setToolTipText(null);\r
return;\r
}\r
\r
}\r
}\r
\r
+ if (row == -1)\r
+ {\r
+ this.setToolTipText(null);\r
+ return;\r
+ }\r
+\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
+ 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
- this.setToolTipText(aa[row].annotations[res].description);\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
- StringBuffer text = new StringBuffer("Sequence position " +\r
- (res + 1) + " " +\r
- aa[row].annotations[res].description);\r
- ap.alignFrame.statusBar.setText(text.toString());\r
+ ap.alignFrame.statusBar.setText(text.toString());\r
+ }\r
+ }\r
+ else\r
+ {\r
+ this.setToolTipText(null);\r
}\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
public void mouseClicked(MouseEvent evt)\r
{\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param g DOCUMENT ME!\r
+ */\r
public void paintComponent(Graphics g)\r
{\r
g.setColor(Color.white);\r
g.fillRect(0, 0, getWidth(), getHeight());\r
\r
- if (fastPaint)\r
+ if (image != null)\r
{\r
- g.drawImage(image, 0, 0, this);\r
- fastPaint = false;\r
-\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
-\r
imgWidth = (av.endRes - av.startRes + 1) * av.charWidth;\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
+ if (image == null || imgWidth != image.getWidth()\r
+ || image.getHeight(this) != getHeight())\r
+ {\r
+ image = new BufferedImage(imgWidth, ap.annotationPanel.getHeight(),\r
+ BufferedImage.TYPE_INT_RGB);\r
+ gg = (Graphics2D) image.getGraphics();\r
+\r
+ if (av.antiAlias)\r
+ {\r
+ gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
+ RenderingHints.VALUE_ANTIALIAS_ON);\r
+ }\r
\r
- gg.setFont(av.getFont());\r
- fm = gg.getFontMetrics();\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
+ 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
-\r
return;\r
}\r
\r
gg.translate( -transX, 0);\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
\r
+ g.setFont(av.getFont());\r
+ if (fm == null)\r
+ {\r
+ fm = g.getFontMetrics();\r
+ }\r
+\r
if ( (av.alignment.getAlignmentAnnotation() == null) ||\r
(av.alignment.getAlignmentAnnotation().length < 1))\r
{\r
g.setColor(Color.white);\r
g.fillRect(0, 0, getWidth(), getHeight());\r
g.setColor(Color.black);\r
- 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
\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
+ int x = 0, y=0;\r
+ int column = 0;\r
+ char lastSS;\r
+ int lastSSX;\r
+ int iconOffset = 0;\r
boolean validRes = false;\r
\r
+ boolean[] graphGroupDrawn = new boolean[aa.length];\r
+\r
//\u03B2 \u03B1\r
for (int i = 0; i < aa.length; i++)\r
{\r
continue;\r
}\r
\r
- if (row.isGraph)\r
+ lastSS = ' ';\r
+ lastSSX = 0;\r
+\r
+ if (row.graph > 0)\r
{\r
+ if (row.graphGroup > -1 && graphGroupDrawn[row.graphGroup])\r
+ {\r
+ continue;\r
+ }\r
+\r
// this is so that we draw the characters below the graph\r
y += row.height;\r
\r
if (row.hasText)\r
{\r
+ iconOffset =av.charHeight -fm.getDescent();\r
y -= av.charHeight;\r
}\r
}\r
-\r
- if (row.hasText)\r
+ else if (row.hasText)\r
{\r
- iconOffset = av.charHeight / 2;\r
+ iconOffset = av.charHeight -fm.getDescent();\r
+\r
}\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
+ y += av.charHeight;\r
+\r
+ g.drawImage(fadedImage,\r
+ 0, y - row.height, imgWidth, y,\r
+ 0, y - row.height, imgWidth, y, this);\r
+ g.setColor(Color.black);\r
+ // g.drawString("Calculating Consensus....",20, y-row.height/2);\r
+\r
+ continue;\r
+ }\r
+ else if (av.updatingConservation && aa[i].label.equals("Conservation"))\r
+ {\r
+\r
+ y += av.charHeight;\r
+ g.drawImage(fadedImage,\r
+ 0, y - row.height, imgWidth, y,\r
+ 0, y - row.height, imgWidth, y, this);\r
+\r
+ g.setColor(Color.black);\r
+ // g.drawString("Calculating Conservation.....",20, y-row.height/2);\r
+\r
+ continue;\r
+ }\r
+ else if (av.updatingConservation && aa[i].label.equals("Quality"))\r
+ {\r
+\r
+ y += av.charHeight;\r
+ g.drawImage(fadedImage,\r
+ 0, y - row.height, imgWidth, y,\r
+ 0, y - row.height, imgWidth, y, this);\r
+ g.setColor(Color.black);\r
+ /// g.drawString("Calculating Quality....",20, y-row.height/2);\r
+\r
+ continue;\r
+ }\r
+\r
+\r
+\r
+ x = 0;\r
+ while (x < endRes - startRes)\r
{\r
- if ( (row.annotations.length <= j) ||\r
- (row.annotations[j] == null))\r
+ if (av.hasHiddenColumns)\r
+ {\r
+ column = av.getColumnSelection().adjustForHiddenColumns(startRes + x);\r
+ if (column > row.annotations.length - 1)\r
+ {\r
+ break;\r
+ }\r
+ }\r
+ else\r
+ {\r
+ column = startRes + x;\r
+ }\r
+\r
+ if ( (row.annotations.length <= column) ||\r
+ (row.annotations[column] == null))\r
{\r
validRes = false;\r
}\r
validRes = true;\r
}\r
\r
- x = (j - startRes) * av.charWidth;\r
-\r
if (activeRow == i)\r
{\r
g.setColor(Color.red);\r
\r
- if (activeRes != null)\r
+ if (av.getColumnSelection() != null)\r
{\r
- for (int n = 0; n < activeRes.size(); n++)\r
+ for (int n = 0; n < av.getColumnSelection().size(); n++)\r
{\r
- int v = Integer.parseInt(activeRes.get(n).toString());\r
+ int v = av.getColumnSelection().columnAt(n);\r
\r
- if (v == j)\r
+ if (v == column)\r
{\r
- g.fillRect( (j - startRes) * av.charWidth, y,\r
- av.charWidth, row.height);\r
+ g.fillRect(x * av.charWidth, y,\r
+ av.charWidth, av.charHeight);\r
}\r
}\r
}\r
}\r
\r
- if (validRes &&\r
- (row.annotations[j].displayCharacter.length() > 0))\r
+ if (av.validCharWidth && validRes\r
+ && row.annotations[column].displayCharacter != null\r
+ && (row.annotations[column].displayCharacter.length() > 0))\r
{\r
+\r
int charOffset = (av.charWidth -\r
- fm.charWidth(row.annotations[j].displayCharacter.\r
- charAt(\r
+ fm.charWidth(row.annotations[column].\r
+ displayCharacter.charAt(\r
0))) / 2;\r
- g.setColor(row.annotations[j].colour);\r
\r
- if (j == 0)\r
+ if (row.annotations[column].colour == null)\r
+ g.setColor(Color.black);\r
+ else\r
+ g.setColor(row.annotations[column].colour);\r
+\r
+ if (column == 0 || row.graph > 0)\r
{\r
- g.drawString(row.annotations[j].displayCharacter,\r
- x, y + iconOffset + 2);\r
+ g.drawString(row.annotations[column].displayCharacter,\r
+ (x * av.charWidth) + charOffset,\r
+ y + iconOffset);\r
}\r
else if (\r
- ( (row.annotations[j - 1] == null) ||\r
- (row.annotations[j].displayCharacter != row.annotations[j -\r
- 1].displayCharacter)))\r
+ row.annotations[column - 1] == null\r
+ || (!row.annotations[column].displayCharacter.equals(\r
+ row.annotations[column - 1].displayCharacter)\r
+ ||\r
+ (row.annotations[column].displayCharacter.length() < 2 &&\r
+ row.annotations[column].secondaryStructure == ' ')))\r
{\r
- g.drawString(row.annotations[j].displayCharacter, x,\r
- y + iconOffset + 2);\r
+ g.drawString(row.annotations[column].displayCharacter,\r
+ x * av.charWidth + charOffset,\r
+ y + iconOffset);\r
}\r
-\r
}\r
\r
if (row.hasIcons)\r
{\r
if (!validRes ||\r
- (row.annotations[j].secondaryStructure != lastSS[i]))\r
+ (row.annotations[column].secondaryStructure != lastSS))\r
{\r
- switch (lastSS[i])\r
+ switch (lastSS)\r
{\r
case 'H':\r
g.setColor(HELIX_COLOUR);\r
- g.fillRoundRect(lastSSX[i], y + 4 + iconOffset,\r
- x - lastSSX[i], 7, 8, 8);\r
-\r
+ 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[i], y + 4 + iconOffset,\r
- x - lastSSX[i] - 4, 7);\r
+ g.fillRect(lastSSX, y + 4 + iconOffset,\r
+ (x * av.charWidth) - lastSSX - 4, 7);\r
g.fillPolygon(new int[]\r
- {x - 4, x - 4, x},\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
\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
+ g.fillRect(lastSSX, y + 6 + iconOffset,\r
+ (x * av.charWidth) - lastSSX, 2);\r
\r
break;\r
}\r
\r
if (validRes)\r
{\r
- lastSS[i] = row.annotations[j].secondaryStructure;\r
+ lastSS = row.annotations[column].secondaryStructure;\r
}\r
else\r
{\r
- lastSS[i] = ' ';\r
+ lastSS = ' ';\r
}\r
\r
- lastSSX[i] = x;\r
+ lastSSX = (x * av.charWidth);\r
}\r
}\r
\r
- if (validRes && row.isGraph)\r
- {\r
- g.setColor(new Color(0, 0, 180));\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
+ column++;\r
+ x++;\r
+ }\r
\r
- g.setColor(row.annotations[j].colour);\r
- g.fillRect(x, y - height, av.charWidth, height);\r
- }\r
+ if (column >= row.annotations.length)\r
+ {\r
+ column = row.annotations.length - 1;\r
}\r
\r
- x += av.charWidth;\r
+ // x ++;\r
\r
if (row.hasIcons)\r
{\r
- switch (lastSS[i])\r
+ switch (lastSS)\r
{\r
case 'H':\r
g.setColor(HELIX_COLOUR);\r
- g.fillRoundRect(lastSSX[i], y + 4 + iconOffset,\r
- x - lastSSX[i], 7, 8, 8);\r
+ 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
- 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
+ if (row.annotations[endRes] == null\r
+ || row.annotations[endRes].secondaryStructure != 'E')\r
+ {\r
+ g.fillRect(lastSSX, y + 4 + iconOffset,\r
+ (x * av.charWidth) - lastSSX - 4, 7);\r
+ g.fillPolygon(new int[]\r
+ { (x * av.charWidth) - 4,\r
+ (x * av.charWidth) - 4,\r
+ (x * av.charWidth)},\r
+ new int[]\r
+ {\r
+ y + iconOffset, y + 14 + iconOffset,\r
+ y + 7 + iconOffset\r
+ }, 3);\r
+ }\r
+ else\r
+ {\r
+ g.fillRect(lastSSX, y + 4 + iconOffset,\r
+ (x + 1) * av.charWidth - lastSSX, 7);\r
+ }\r
break;\r
\r
default:\r
g.setColor(Color.gray);\r
- g.fillRect(lastSSX[i], y + 6 + iconOffset, x - lastSSX[i], 2);\r
+ g.fillRect(lastSSX, y + 6 + iconOffset,\r
+ (x * av.charWidth) - lastSSX, 2);\r
\r
break;\r
}\r
}\r
\r
- if (row.isGraph && row.hasText)\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
+ if (row.graph > 0 && row.hasText)\r
{\r
y += av.charHeight;\r
}\r
\r
- if (!row.isGraph)\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
+ 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 || 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
\r
- int x = 0;\r
+ int x = 0, height;\r
\r
- for (int j = 0; j < aa.annotations.length; j++)\r
+ for (int j = sRes; j < eRes; j++)\r
{\r
- g.setColor(new Color(0, 0, 180));\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
- int height = (int) ( (aa.annotations[j].value / aa.graphMax) *\r
- GRAPH_HEIGHT);\r
- g.fillRect(x, y - height, av.charWidth, height);\r
+ height = (int) ( (aa.annotations[j].value / aa.graphMax) * y);\r
+ if (height > y)\r
+ {\r
+ height = y;\r
+ }\r
+\r
+ g.fillRect(x, y - height, av.charWidth, height);\r
+ }\r
x += av.charWidth;\r
}\r
}\r
+\r
}\r
git://source.jalview.org / jalview.git / blobdiff