*/\r
package jalview.gui;\r
\r
-import java.util.*;\r
+import jalview.analysis.*;\r
+\r
+import jalview.datamodel.*;\r
+\r
+import jalview.schemes.*;\r
+\r
+import jalview.util.*;\r
\r
import java.awt.*;\r
import java.awt.event.*;\r
import java.awt.print.*;\r
+\r
+import java.util.*;\r
+\r
import javax.swing.*;\r
\r
-import jalview.analysis.*;\r
-import jalview.datamodel.*;\r
-import jalview.schemes.*;\r
-import jalview.util.*;\r
\r
-public class TreeCanvas\r
- extends JPanel implements MouseListener, Runnable,\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class TreeCanvas extends JPanel implements MouseListener, Runnable,\r
Printable\r
{\r
- public static final String PLACEHOLDER = " * ";\r
- NJTree tree;\r
- JScrollPane scrollPane;\r
- AlignViewport av;\r
- Font font;\r
- int fontSize = 12;\r
- boolean fitToWindow = true;\r
- boolean showDistances = false;\r
- boolean showBootstrap = false;\r
- boolean markPlaceholders = false;\r
- int offx = 20;\r
- int offy = 20;\r
- float threshold;\r
- String longestName;\r
- int labelLength = -1;\r
-\r
- //RubberbandRectangle rubberband;\r
- Vector listeners;\r
- Hashtable nameHash = new Hashtable();\r
- Hashtable nodeHash = new Hashtable();\r
-\r
- public TreeCanvas(AlignViewport av, NJTree tree, JScrollPane scroller,\r
- String label)\r
- {\r
- this.av = av;\r
- this.tree = tree;\r
- scrollPane = scroller;\r
- addMouseListener(this);\r
- tree.findHeight(tree.getTopNode());\r
- longestName = label;\r
-\r
- PaintRefresher.Register(this, av.alignment);\r
- }\r
-\r
- public void TreeSelectionChanged(Sequence sequence)\r
- {\r
- SequenceGroup selected = av.getSelectionGroup();\r
-\r
- if (selected == null)\r
+ /** DOCUMENT ME!! */\r
+ public static final String PLACEHOLDER = " * ";\r
+ NJTree tree;\r
+ JScrollPane scrollPane;\r
+ AlignViewport av;\r
+ Font font;\r
+ int fontSize = 12;\r
+ boolean fitToWindow = true;\r
+ boolean showDistances = false;\r
+ boolean showBootstrap = false;\r
+ boolean markPlaceholders = false;\r
+ int offx = 20;\r
+ int offy = 20;\r
+ float threshold;\r
+ String longestName;\r
+ int labelLength = -1;\r
+\r
+ //RubberbandRectangle rubberband;\r
+ Vector listeners;\r
+ Hashtable nameHash = new Hashtable();\r
+ Hashtable nodeHash = new Hashtable();\r
+\r
+ /**\r
+ * Creates a new TreeCanvas object.\r
+ *\r
+ * @param av DOCUMENT ME!\r
+ * @param tree DOCUMENT ME!\r
+ * @param scroller DOCUMENT ME!\r
+ * @param label DOCUMENT ME!\r
+ */\r
+ public TreeCanvas(AlignViewport av, NJTree tree, JScrollPane scroller,\r
+ String label)\r
{\r
- selected = new SequenceGroup();\r
- av.setSelectionGroup(selected);\r
+ this.av = av;\r
+ this.tree = tree;\r
+ scrollPane = scroller;\r
+ addMouseListener(this);\r
+ tree.findHeight(tree.getTopNode());\r
+ longestName = label;\r
+\r
+ PaintRefresher.Register(this, av.alignment);\r
}\r
\r
- selected.setEndRes(av.alignment.getWidth());\r
- selected.addOrRemove(sequence, true);\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param sequence DOCUMENT ME!\r
+ */\r
+ public void TreeSelectionChanged(Sequence sequence)\r
+ {\r
+ SequenceGroup selected = av.getSelectionGroup();\r
+\r
+ if (selected == null)\r
+ {\r
+ selected = new SequenceGroup();\r
+ av.setSelectionGroup(selected);\r
+ }\r
\r
- PaintRefresher.Refresh(this, av.alignment);\r
- repaint();\r
- }\r
+ selected.setEndRes(av.alignment.getWidth());\r
+ selected.addOrRemove(sequence, true);\r
\r
- public void setTree(NJTree tree)\r
- {\r
- this.tree = tree;\r
- tree.findHeight(tree.getTopNode());\r
- }\r
+ PaintRefresher.Refresh(this, av.alignment);\r
+ repaint();\r
+ }\r
\r
- public void drawNode(Graphics g, SequenceNode node, float chunk,\r
- float scale, int width, int offx, int offy)\r
- {\r
- if (node == null)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param tree DOCUMENT ME!\r
+ */\r
+ public void setTree(NJTree tree)\r
{\r
- return;\r
+ this.tree = tree;\r
+ tree.findHeight(tree.getTopNode());\r
}\r
\r
- if ( (node.left() == null) && (node.right() == null))\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param g DOCUMENT ME!\r
+ * @param node DOCUMENT ME!\r
+ * @param chunk DOCUMENT ME!\r
+ * @param scale DOCUMENT ME!\r
+ * @param width DOCUMENT ME!\r
+ * @param offx DOCUMENT ME!\r
+ * @param offy DOCUMENT ME!\r
+ */\r
+ public void drawNode(Graphics g, SequenceNode node, float chunk,\r
+ float scale, int width, int offx, int offy)\r
{\r
- // Drawing leaf node\r
- float height = node.height;\r
- float dist = node.dist;\r
-\r
- int xstart = (int) ( (height - dist) * scale) + offx;\r
- int xend = (int) (height * scale) + offx;\r
-\r
- int ypos = (int) (node.ycount * chunk) + offy;\r
-\r
- if (node.element() instanceof SequenceI)\r
- {\r
- if ( ( (SequenceI) ( (SequenceNode) node).element()).getColor() ==\r
- Color.white)\r
- {\r
- g.setColor(Color.black);\r
- }\r
- else\r
+ if (node == null)\r
{\r
- g.setColor( ( (SequenceI) ( (SequenceNode) node).element()).getColor()\r
- .darker());\r
+ return;\r
}\r
- }\r
- else\r
- {\r
- g.setColor(Color.black);\r
- }\r
-\r
- // Draw horizontal line\r
- g.drawLine(xstart, ypos, xend, ypos);\r
-\r
- String nodeLabel = "";\r
\r
- if (showDistances && (node.dist > 0))\r
- {\r
- nodeLabel = new Format("%5.2f").form(node.dist);\r
- }\r
-\r
- if (showBootstrap)\r
- {\r
- if (showDistances)\r
+ if ((node.left() == null) && (node.right() == null))\r
{\r
- nodeLabel = nodeLabel + " : ";\r
+ // Drawing leaf node\r
+ float height = node.height;\r
+ float dist = node.dist;\r
+\r
+ int xstart = (int) ((height - dist) * scale) + offx;\r
+ int xend = (int) (height * scale) + offx;\r
+\r
+ int ypos = (int) (node.ycount * chunk) + offy;\r
+\r
+ if (node.element() instanceof SequenceI)\r
+ {\r
+ if (((SequenceI) ((SequenceNode) node).element()).getColor() == Color.white)\r
+ {\r
+ g.setColor(Color.black);\r
+ }\r
+ else\r
+ {\r
+ g.setColor(((SequenceI) ((SequenceNode) node).element()).getColor()\r
+ .darker());\r
+ }\r
+ }\r
+ else\r
+ {\r
+ g.setColor(Color.black);\r
+ }\r
+\r
+ // Draw horizontal line\r
+ g.drawLine(xstart, ypos, xend, ypos);\r
+\r
+ String nodeLabel = "";\r
+\r
+ if (showDistances && (node.dist > 0))\r
+ {\r
+ nodeLabel = new Format("%5.2f").form(node.dist);\r
+ }\r
+\r
+ if (showBootstrap)\r
+ {\r
+ if (showDistances)\r
+ {\r
+ nodeLabel = nodeLabel + " : ";\r
+ }\r
+\r
+ nodeLabel = nodeLabel + String.valueOf(node.getBootstrap());\r
+ }\r
+\r
+ if (!nodeLabel.equals(""))\r
+ {\r
+ g.drawString(nodeLabel, xstart, ypos - 10);\r
+ }\r
+\r
+ String name = (markPlaceholders && node.isPlaceholder())\r
+ ? (PLACEHOLDER + node.getName()) : node.getName();\r
+ FontMetrics fm = g.getFontMetrics(font);\r
+ int charWidth = fm.stringWidth(name) + 3;\r
+ int charHeight = fm.getHeight();\r
+\r
+ Rectangle rect = new Rectangle(xend + 20, ypos - charHeight,\r
+ charWidth, charHeight);\r
+\r
+ nameHash.put((SequenceI) node.element(), rect);\r
+\r
+ // Colour selected leaves differently\r
+ SequenceGroup selected = av.getSelectionGroup();\r
+\r
+ if ((selected != null) &&\r
+ selected.sequences.contains((SequenceI) node.element()))\r
+ {\r
+ g.setColor(Color.gray);\r
+\r
+ g.fillRect(xend + 10, ypos - charHeight + 3, charWidth,\r
+ charHeight);\r
+ g.setColor(Color.white);\r
+ }\r
+\r
+ g.drawString(name, xend + 10, ypos);\r
+ g.setColor(Color.black);\r
}\r
+ else\r
+ {\r
+ drawNode(g, (SequenceNode) node.left(), chunk, scale, width, offx,\r
+ offy);\r
+ drawNode(g, (SequenceNode) node.right(), chunk, scale, width, offx,\r
+ offy);\r
\r
- nodeLabel = nodeLabel + String.valueOf(node.getBootstrap());\r
- }\r
-\r
- if (!nodeLabel.equals(""))\r
- {\r
- g.drawString(nodeLabel, xstart, ypos - 10);\r
- }\r
+ float height = node.height;\r
+ float dist = node.dist;\r
\r
- String name = (markPlaceholders && node.isPlaceholder())\r
- ? (PLACEHOLDER + node.getName()) : node.getName();\r
- FontMetrics fm = g.getFontMetrics(font);\r
- int charWidth = fm.stringWidth(name) + 3;\r
- int charHeight = fm.getHeight();\r
+ int xstart = (int) ((height - dist) * scale) + offx;\r
+ int xend = (int) (height * scale) + offx;\r
+ int ypos = (int) (node.ycount * chunk) + offy;\r
\r
- Rectangle rect = new Rectangle(xend + 20, ypos - charHeight,\r
- charWidth, charHeight);\r
+ g.setColor(((SequenceNode) node).color.darker());\r
\r
- nameHash.put( (SequenceI) node.element(), rect);\r
+ // Draw horizontal line\r
+ g.drawLine(xstart, ypos, xend, ypos);\r
+ g.fillRect(xend - 2, ypos - 2, 4, 4);\r
\r
- // Colour selected leaves differently\r
- SequenceGroup selected = av.getSelectionGroup();\r
+ int ystart = (int) (((SequenceNode) node.left()).ycount * chunk) +\r
+ offy;\r
+ int yend = (int) (((SequenceNode) node.right()).ycount * chunk) +\r
+ offy;\r
\r
- if ( (selected != null) &&\r
- selected.sequences.contains( (SequenceI) node.element()))\r
- {\r
- g.setColor(Color.gray);\r
+ Rectangle pos = new Rectangle(xend - 2, ypos - 2, 5, 5);\r
+ nodeHash.put(node, pos);\r
\r
- g.fillRect(xend + 10, ypos - charHeight + 3, charWidth,\r
- charHeight);\r
- g.setColor(Color.white);\r
- }\r
+ g.drawLine((int) (height * scale) + offx, ystart,\r
+ (int) (height * scale) + offx, yend);\r
\r
- g.drawString(name, xend + 10, ypos);\r
- g.setColor(Color.black);\r
+ if (showDistances && (node.dist > 0))\r
+ {\r
+ g.drawString(new Format("%5.2f").form(node.dist), xstart,\r
+ ypos - 5);\r
+ }\r
+ }\r
}\r
- else\r
- {\r
- drawNode(g, (SequenceNode) node.left(), chunk, scale, width, offx,\r
- offy);\r
- drawNode(g, (SequenceNode) node.right(), chunk, scale, width, offx,\r
- offy);\r
\r
- float height = node.height;\r
- float dist = node.dist;\r
-\r
- int xstart = (int) ( (height - dist) * scale) + offx;\r
- int xend = (int) (height * scale) + offx;\r
- int ypos = (int) (node.ycount * chunk) + offy;\r
-\r
- g.setColor( ( (SequenceNode) node).color.darker());\r
-\r
- // Draw horizontal line\r
- g.drawLine(xstart, ypos, xend, ypos);\r
- g.fillRect(xend - 2, ypos - 2, 4, 4);\r
-\r
- int ystart = (int) ( ( (SequenceNode) node.left()).ycount * chunk) +\r
- offy;\r
- int yend = (int) ( ( (SequenceNode) node.right()).ycount * chunk) +\r
- offy;\r
-\r
- Rectangle pos = new Rectangle(xend - 2, ypos - 2, 5, 5);\r
- nodeHash.put(node, pos);\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param x DOCUMENT ME!\r
+ * @param y DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public Object findElement(int x, int y)\r
+ {\r
+ Enumeration keys = nameHash.keys();\r
\r
- g.drawLine( (int) (height * scale) + offx, ystart,\r
- (int) (height * scale) + offx, yend);\r
+ while (keys.hasMoreElements())\r
+ {\r
+ Object ob = keys.nextElement();\r
+ Rectangle rect = (Rectangle) nameHash.get(ob);\r
+\r
+ if ((x >= rect.x) && (x <= (rect.x + rect.width)) && (y >= rect.y) &&\r
+ (y <= (rect.y + rect.height)))\r
+ {\r
+ return ob;\r
+ }\r
+ }\r
\r
- if (showDistances && (node.dist > 0))\r
- {\r
- g.drawString(new Format("%5.2f").form(node.dist), xstart,\r
- ypos - 5);\r
- }\r
- }\r
- }\r
+ keys = nodeHash.keys();\r
\r
- public Object findElement(int x, int y)\r
- {\r
- Enumeration keys = nameHash.keys();\r
+ while (keys.hasMoreElements())\r
+ {\r
+ Object ob = keys.nextElement();\r
+ Rectangle rect = (Rectangle) nodeHash.get(ob);\r
+\r
+ if ((x >= rect.x) && (x <= (rect.x + rect.width)) && (y >= rect.y) &&\r
+ (y <= (rect.y + rect.height)))\r
+ {\r
+ return ob;\r
+ }\r
+ }\r
\r
- while (keys.hasMoreElements())\r
- {\r
- Object ob = keys.nextElement();\r
- Rectangle rect = (Rectangle) nameHash.get(ob);\r
-\r
- if ( (x >= rect.x) && (x <= (rect.x + rect.width)) && (y >= rect.y) &&\r
- (y <= (rect.y + rect.height)))\r
- {\r
- return ob;\r
- }\r
+ return null;\r
}\r
\r
- keys = nodeHash.keys();\r
-\r
- while (keys.hasMoreElements())\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param pickBox DOCUMENT ME!\r
+ */\r
+ public void pickNodes(Rectangle pickBox)\r
{\r
- Object ob = keys.nextElement();\r
- Rectangle rect = (Rectangle) nodeHash.get(ob);\r
-\r
- if ( (x >= rect.x) && (x <= (rect.x + rect.width)) && (y >= rect.y) &&\r
- (y <= (rect.y + rect.height)))\r
- {\r
- return ob;\r
- }\r
- }\r
+ int width = getWidth();\r
+ int height = getHeight();\r
\r
- return null;\r
- }\r
+ SequenceNode top = tree.getTopNode();\r
\r
- public void pickNodes(Rectangle pickBox)\r
- {\r
- int width = getWidth();\r
- int height = getHeight();\r
+ float wscale = (float) ((width * .8) - (offx * 2)) / tree.getMaxHeight();\r
\r
- SequenceNode top = tree.getTopNode();\r
+ if (top.count == 0)\r
+ {\r
+ top.count = ((SequenceNode) top.left()).count +\r
+ ((SequenceNode) top.right()).count;\r
+ }\r
\r
- float wscale = (float) ( (width * .8) - (offx * 2)) / tree.getMaxHeight();\r
+ float chunk = (float) (height - (offy * 2)) / top.count;\r
\r
- if (top.count == 0)\r
- {\r
- top.count = ( (SequenceNode) top.left()).count +\r
- ( (SequenceNode) top.right()).count;\r
+ pickNode(pickBox, top, chunk, wscale, width, offx, offy);\r
}\r
\r
- float chunk = (float) (height - (offy * 2)) / top.count;\r
-\r
- pickNode(pickBox, top, chunk, wscale, width, offx, offy);\r
- }\r
-\r
- public void pickNode(Rectangle pickBox, SequenceNode node, float chunk,\r
- float scale, int width, int offx, int offy)\r
- {\r
- if (node == null)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param pickBox DOCUMENT ME!\r
+ * @param node DOCUMENT ME!\r
+ * @param chunk DOCUMENT ME!\r
+ * @param scale DOCUMENT ME!\r
+ * @param width DOCUMENT ME!\r
+ * @param offx DOCUMENT ME!\r
+ * @param offy DOCUMENT ME!\r
+ */\r
+ public void pickNode(Rectangle pickBox, SequenceNode node, float chunk,\r
+ float scale, int width, int offx, int offy)\r
{\r
- return;\r
+ if (node == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ if ((node.left() == null) && (node.right() == null))\r
+ {\r
+ float height = node.height;\r
+ float dist = node.dist;\r
+\r
+ int xstart = (int) ((height - dist) * scale) + offx;\r
+ int xend = (int) (height * scale) + offx;\r
+\r
+ int ypos = (int) (node.ycount * chunk) + offy;\r
+\r
+ if (pickBox.contains(new Point(xend, ypos)))\r
+ {\r
+ if (node.element() instanceof SequenceI)\r
+ {\r
+ SequenceI seq = (SequenceI) node.element();\r
+ SequenceGroup sg = av.getSelectionGroup();\r
+\r
+ if (sg != null)\r
+ {\r
+ sg.addOrRemove(seq, true);\r
+ }\r
+ }\r
+ }\r
+ }\r
+ else\r
+ {\r
+ pickNode(pickBox, (SequenceNode) node.left(), chunk, scale, width,\r
+ offx, offy);\r
+ pickNode(pickBox, (SequenceNode) node.right(), chunk, scale, width,\r
+ offx, offy);\r
+ }\r
}\r
\r
- if ( (node.left() == null) && (node.right() == null))\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param node DOCUMENT ME!\r
+ * @param c DOCUMENT ME!\r
+ */\r
+ public void setColor(SequenceNode node, Color c)\r
{\r
- float height = node.height;\r
- float dist = node.dist;\r
-\r
- int xstart = (int) ( (height - dist) * scale) + offx;\r
- int xend = (int) (height * scale) + offx;\r
-\r
- int ypos = (int) (node.ycount * chunk) + offy;\r
+ if (node == null)\r
+ {\r
+ return;\r
+ }\r
\r
- if (pickBox.contains(new Point(xend, ypos)))\r
- {\r
- if (node.element() instanceof SequenceI)\r
+ if ((node.left() == null) && (node.right() == null))\r
{\r
- SequenceI seq = (SequenceI) node.element();\r
- SequenceGroup sg = av.getSelectionGroup();\r
+ node.color = c;\r
\r
- if (sg != null)\r
- {\r
- sg.addOrRemove(seq, true);\r
- }\r
+ if (node.element() instanceof SequenceI)\r
+ {\r
+ ((SequenceI) node.element()).setColor(c);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ node.color = c;\r
+ setColor((SequenceNode) node.left(), c);\r
+ setColor((SequenceNode) node.right(), c);\r
}\r
- }\r
- }\r
- else\r
- {\r
- pickNode(pickBox, (SequenceNode) node.left(), chunk, scale, width,\r
- offx, offy);\r
- pickNode(pickBox, (SequenceNode) node.right(), chunk, scale, width,\r
- offx, offy);\r
}\r
- }\r
\r
- public void setColor(SequenceNode node, Color c)\r
- {\r
- if (node == null)\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
+ void startPrinting()\r
{\r
- return;\r
+ Thread thread = new Thread(this);\r
+ thread.start();\r
}\r
\r
- if ( (node.left() == null) && (node.right() == null))\r
+ // put printing in a thread to avoid painting problems\r
+ public void run()\r
{\r
- node.color = c;\r
+ PrinterJob printJob = PrinterJob.getPrinterJob();\r
+ PageFormat pf = printJob.pageDialog(printJob.defaultPage());\r
\r
- if (node.element() instanceof SequenceI)\r
- {\r
- ( (SequenceI) node.element()).setColor(c);\r
- }\r
- }\r
- else\r
- {\r
- node.color = c;\r
- setColor( (SequenceNode) node.left(), c);\r
- setColor( (SequenceNode) node.right(), c);\r
+ printJob.setPrintable(this, pf);\r
+\r
+ if (printJob.printDialog())\r
+ {\r
+ try\r
+ {\r
+ printJob.print();\r
+ }\r
+ catch (Exception PrintException)\r
+ {\r
+ PrintException.printStackTrace();\r
+ }\r
+ }\r
}\r
- }\r
\r
- void startPrinting()\r
- {\r
- Thread thread = new Thread(this);\r
- thread.start();\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param pg DOCUMENT ME!\r
+ * @param pf DOCUMENT ME!\r
+ * @param pi DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ *\r
+ * @throws PrinterException DOCUMENT ME!\r
+ */\r
+ public int print(Graphics pg, PageFormat pf, int pi)\r
+ throws PrinterException\r
+ {\r
+ pg.setFont(font);\r
+ pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());\r
\r
- // put printing in a thread to avoid painting problems\r
- public void run()\r
- {\r
- PrinterJob printJob = PrinterJob.getPrinterJob();\r
- PageFormat pf = printJob.pageDialog(printJob.defaultPage());\r
+ int pwidth = (int) pf.getImageableWidth();\r
+ int pheight = (int) pf.getImageableHeight();\r
\r
- printJob.setPrintable(this, pf);\r
+ int noPages = getHeight() / pheight;\r
\r
- if (printJob.printDialog())\r
- {\r
- try\r
- {\r
- printJob.print();\r
- }\r
- catch (Exception PrintException)\r
- {\r
- PrintException.printStackTrace();\r
- }\r
- }\r
- }\r
+ if (pi > noPages)\r
+ {\r
+ return Printable.NO_SUCH_PAGE;\r
+ }\r
\r
- public int print(Graphics pg, PageFormat pf, int pi)\r
- throws PrinterException\r
- {\r
- pg.setFont(font);\r
- pg.translate( (int) pf.getImageableX(), (int) pf.getImageableY());\r
+ if (pwidth > getWidth())\r
+ {\r
+ pwidth = getWidth();\r
+ }\r
\r
- int pwidth = (int) pf.getImageableWidth();\r
- int pheight = (int) pf.getImageableHeight();\r
+ if (fitToWindow)\r
+ {\r
+ if (pheight > getHeight())\r
+ {\r
+ pheight = getHeight();\r
+ }\r
\r
- int noPages = getHeight() / pheight;\r
+ noPages = 0;\r
+ }\r
+ else\r
+ {\r
+ FontMetrics fm = pg.getFontMetrics(font);\r
+ int height = fm.getHeight() * nameHash.size();\r
+ pg.translate(0, -pi * pheight);\r
+ pg.setClip(0, pi * pheight, pwidth, (pi * pheight) + pheight);\r
+\r
+ // translate number of pages,\r
+ // height is screen size as this is the\r
+ // non overlapping text size\r
+ pheight = height;\r
+ }\r
\r
- if (pi > noPages)\r
- {\r
- return Printable.NO_SUCH_PAGE;\r
- }\r
+ draw(pg, pwidth, pheight);\r
\r
- if (pwidth > getWidth())\r
- {\r
- pwidth = getWidth();\r
+ return Printable.PAGE_EXISTS;\r
}\r
\r
- if (fitToWindow)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param g DOCUMENT ME!\r
+ */\r
+ public void paintComponent(Graphics g)\r
{\r
- if (pheight > getHeight())\r
- {\r
- pheight = getHeight();\r
- }\r
+ super.paintComponent(g);\r
+ font = new Font("Verdana", Font.PLAIN, fontSize);\r
+ g.setFont(font);\r
\r
- noPages = 0;\r
- }\r
- else\r
- {\r
- FontMetrics fm = pg.getFontMetrics(font);\r
- int height = fm.getHeight() * nameHash.size();\r
- pg.translate(0, -pi * pheight);\r
- pg.setClip(0, pi * pheight, pwidth, (pi * pheight) + pheight);\r
-\r
- // translate number of pages,\r
- // height is screen size as this is the\r
- // non overlapping text size\r
- pheight = height;\r
- }\r
+ FontMetrics fm = g.getFontMetrics(font);\r
\r
- draw(pg, pwidth, pheight);\r
-\r
- return Printable.PAGE_EXISTS;\r
- }\r
+ if (nameHash.size() == 0)\r
+ {\r
+ repaint();\r
+ }\r
\r
- public void paintComponent(Graphics g)\r
- {\r
- super.paintComponent(g);\r
- font = new Font("Verdana", Font.PLAIN, fontSize);\r
- g.setFont(font);\r
+ if (fitToWindow ||\r
+ (!fitToWindow &&\r
+ (scrollPane.getHeight() > ((fm.getHeight() * nameHash.size()) +\r
+ offy))))\r
+ {\r
+ draw(g, scrollPane.getWidth(), scrollPane.getHeight());\r
+ setPreferredSize(null);\r
+ }\r
+ else\r
+ {\r
+ setPreferredSize(new Dimension(scrollPane.getWidth(),\r
+ fm.getHeight() * nameHash.size()));\r
+ draw(g, scrollPane.getWidth(), fm.getHeight() * nameHash.size());\r
+ }\r
\r
- FontMetrics fm = g.getFontMetrics(font);\r
+ scrollPane.revalidate();\r
+ }\r
\r
- if (nameHash.size() == 0)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public int getFontSize()\r
{\r
- repaint();\r
+ return fontSize;\r
}\r
\r
- if (fitToWindow ||\r
- (!fitToWindow &&\r
- (scrollPane.getHeight() > ( (fm.getHeight() * nameHash.size()) +\r
- offy))))\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param fontSize DOCUMENT ME!\r
+ */\r
+ public void setFontSize(int fontSize)\r
{\r
- draw(g, scrollPane.getWidth(), scrollPane.getHeight());\r
- setPreferredSize(null);\r
+ this.fontSize = fontSize;\r
+ repaint();\r
}\r
- else\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param g1 DOCUMENT ME!\r
+ * @param width DOCUMENT ME!\r
+ * @param height DOCUMENT ME!\r
+ */\r
+ public void draw(Graphics g1, int width, int height)\r
{\r
- setPreferredSize(new Dimension(scrollPane.getWidth(),\r
- fm.getHeight() * nameHash.size()));\r
- draw(g, scrollPane.getWidth(), fm.getHeight() * nameHash.size());\r
- }\r
+ Graphics2D g2 = (Graphics2D) g1;\r
+ g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
+ RenderingHints.VALUE_ANTIALIAS_ON);\r
+ g2.setColor(Color.white);\r
+ g2.fillRect(0, 0, width, height);\r
\r
- scrollPane.revalidate();\r
- }\r
+ labelLength = g2.getFontMetrics(font).stringWidth(longestName) + 20; //20 allows for scrollbar\r
\r
- public int getFontSize()\r
- {\r
- return fontSize;\r
- }\r
+ float wscale = (float) (width - labelLength - (offx * 2)) / tree.getMaxHeight();\r
\r
- public void setFontSize(int fontSize)\r
- {\r
- this.fontSize = fontSize;\r
- repaint();\r
- }\r
+ SequenceNode top = tree.getTopNode();\r
\r
- public void draw(Graphics g1, int width, int height)\r
- {\r
- Graphics2D g2 = (Graphics2D) g1;\r
- g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
- RenderingHints.VALUE_ANTIALIAS_ON);\r
- g2.setColor(Color.white);\r
- g2.fillRect(0, 0, width, height);\r
+ if (top.count == 0)\r
+ {\r
+ top.count = ((SequenceNode) top.left()).count +\r
+ ((SequenceNode) top.right()).count;\r
+ }\r
\r
- labelLength = g2.getFontMetrics(font).stringWidth(longestName) + 20; //20 allows for scrollbar\r
+ float chunk = (float) (height - (offy * 2)) / top.count;\r
\r
- float wscale = (float) (width - labelLength - (offx * 2)) /\r
- tree.getMaxHeight();\r
+ drawNode(g2, tree.getTopNode(), chunk, wscale, width, offx, offy);\r
\r
- SequenceNode top = tree.getTopNode();\r
+ if (threshold != 0)\r
+ {\r
+ if (av.getCurrentTree() == tree)\r
+ {\r
+ g2.setColor(Color.red);\r
+ }\r
+ else\r
+ {\r
+ g2.setColor(Color.gray);\r
+ }\r
+\r
+ int x = (int) ((threshold * (float) (getWidth() - labelLength -\r
+ (2 * offx))) + offx);\r
+\r
+ g2.drawLine(x, 0, x, getHeight());\r
+ }\r
+ }\r
\r
- if (top.count == 0)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void mouseReleased(MouseEvent e)\r
{\r
- top.count = ( (SequenceNode) top.left()).count +\r
- ( (SequenceNode) top.right()).count;\r
}\r
\r
- float chunk = (float) (height - (offy * 2)) / top.count;\r
-\r
- drawNode(g2, tree.getTopNode(), chunk, wscale, width, offx, offy);\r
-\r
- if (threshold != 0)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void mouseEntered(MouseEvent e)\r
{\r
- if (av.getCurrentTree() == tree)\r
- {\r
- g2.setColor(Color.red);\r
- }\r
- else\r
- {\r
- g2.setColor(Color.gray);\r
- }\r
-\r
- int x = (int) ( (threshold * (float) (getWidth() - labelLength -\r
- (2 * offx))) + offx);\r
-\r
- g2.drawLine(x, 0, x, getHeight());\r
}\r
- }\r
-\r
- public void mouseReleased(MouseEvent e)\r
- {\r
- }\r
-\r
- public void mouseEntered(MouseEvent e)\r
- {\r
- }\r
-\r
- public void mouseExited(MouseEvent e)\r
- {\r
- }\r
-\r
- public void mouseClicked(MouseEvent e)\r
- {\r
- }\r
\r
- public void mousePressed(MouseEvent e)\r
- {\r
- av.setCurrentTree(tree);\r
-\r
- int x = e.getX();\r
- int y = e.getY();\r
-\r
- Object ob = findElement(x, y);\r
-\r
- if (ob instanceof SequenceI)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void mouseExited(MouseEvent e)\r
{\r
- TreeSelectionChanged( (Sequence) ob);\r
- repaint();\r
-\r
- return;\r
}\r
- else if (ob instanceof SequenceNode)\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void mouseClicked(MouseEvent e)\r
{\r
- SequenceNode tmpnode = (SequenceNode) ob;\r
- tree.swapNodes(tmpnode);\r
- tree.reCount(tree.getTopNode());\r
- tree.findHeight(tree.getTopNode());\r
}\r
- else\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void mousePressed(MouseEvent e)\r
{\r
- // Find threshold\r
- if (tree.getMaxHeight() != 0)\r
- {\r
- threshold = (float) (x - offx) / (float) (getWidth() -\r
- labelLength - (2 * offx));\r
+ av.setCurrentTree(tree);\r
\r
- tree.getGroups().removeAllElements();\r
- tree.groupNodes(tree.getTopNode(), threshold);\r
- setColor(tree.getTopNode(), Color.black);\r
+ int x = e.getX();\r
+ int y = e.getY();\r
\r
- av.setSelectionGroup(null);\r
- av.alignment.deleteAllGroups();\r
+ Object ob = findElement(x, y);\r
\r
- for (int i = 0; i < tree.getGroups().size(); i++)\r
+ if (ob instanceof SequenceI)\r
{\r
- Color col = new Color( (int) (Math.random() * 255),\r
- (int) (Math.random() * 255),\r
- (int) (Math.random() * 255));\r
- setColor( (SequenceNode) tree.getGroups().elementAt(i),\r
- col.brighter());\r
-\r
- Vector l = tree.findLeaves( (SequenceNode) tree.getGroups()\r
- .elementAt(i),\r
- new Vector());\r
-\r
- Vector sequences = new Vector();\r
- for (int j = 0; j < l.size(); j++)\r
- {\r
- SequenceI s1 = (SequenceI) ( (SequenceNode) l.elementAt(j)).element();\r
- if (!sequences.contains(s1))\r
- sequences.addElement(s1);\r
-\r
- }\r
+ TreeSelectionChanged((Sequence) ob);\r
+ repaint();\r
\r
- ColourSchemeI cs = ColourSchemeProperty.getColour(sequences, av.alignment.getWidth(),\r
- ColourSchemeProperty.getColourName(av.getGlobalColourScheme()));\r
-\r
- SequenceGroup sg = new SequenceGroup(sequences, "TreeGroup",\r
- cs, true, true,\r
- false, 0, av.alignment.getWidth());\r
-\r
- if(sg.cs !=null)\r
- ( (ResidueColourScheme) sg.cs).setThreshold(25);\r
-\r
-\r
- if (av.getGlobalColourScheme() instanceof ConservationColourScheme)\r
- {\r
- ConservationColourScheme ccs = (ConservationColourScheme) av.\r
- getGlobalColourScheme();\r
- Conservation c = new Conservation("Group",\r
- ResidueProperties.propHash, 3,\r
- sg.sequences,\r
- sg.getStartRes(), sg.getEndRes());\r
+ return;\r
+ }\r
+ else if (ob instanceof SequenceNode)\r
+ {\r
+ SequenceNode tmpnode = (SequenceNode) ob;\r
+ tree.swapNodes(tmpnode);\r
+ tree.reCount(tree.getTopNode());\r
+ tree.findHeight(tree.getTopNode());\r
+ }\r
+ else\r
+ {\r
+ // Find threshold\r
+ if (tree.getMaxHeight() != 0)\r
+ {\r
+ threshold = (float) (x - offx) / (float) (getWidth() -\r
+ labelLength - (2 * offx));\r
+\r
+ tree.getGroups().removeAllElements();\r
+ tree.groupNodes(tree.getTopNode(), threshold);\r
+ setColor(tree.getTopNode(), Color.black);\r
+\r
+ av.setSelectionGroup(null);\r
+ av.alignment.deleteAllGroups();\r
+\r
+ for (int i = 0; i < tree.getGroups().size(); i++)\r
+ {\r
+ Color col = new Color((int) (Math.random() * 255),\r
+ (int) (Math.random() * 255),\r
+ (int) (Math.random() * 255));\r
+ setColor((SequenceNode) tree.getGroups().elementAt(i),\r
+ col.brighter());\r
+\r
+ Vector l = tree.findLeaves((SequenceNode) tree.getGroups()\r
+ .elementAt(i),\r
+ new Vector());\r
+\r
+ Vector sequences = new Vector();\r
+\r
+ for (int j = 0; j < l.size(); j++)\r
+ {\r
+ SequenceI s1 = (SequenceI) ((SequenceNode) l.elementAt(j)).element();\r
+\r
+ if (!sequences.contains(s1))\r
+ {\r
+ sequences.addElement(s1);\r
+ }\r
+ }\r
+\r
+ ColourSchemeI cs = ColourSchemeProperty.getColour(sequences,\r
+ av.alignment.getWidth(),\r
+ ColourSchemeProperty.getColourName(\r
+ av.getGlobalColourScheme()));\r
+\r
+ SequenceGroup sg = new SequenceGroup(sequences,\r
+ "TreeGroup", cs, true, true, false, 0,\r
+ av.alignment.getWidth());\r
+\r
+ if (sg.cs != null)\r
+ {\r
+ ((ResidueColourScheme) sg.cs).setThreshold(25);\r
+ }\r
+\r
+ if (av.getGlobalColourScheme() instanceof ConservationColourScheme)\r
+ {\r
+ ConservationColourScheme ccs = (ConservationColourScheme) av.getGlobalColourScheme();\r
+ Conservation c = new Conservation("Group",\r
+ ResidueProperties.propHash, 3, sg.sequences,\r
+ sg.getStartRes(), sg.getEndRes());\r
+\r
+ c.calculate();\r
+ c.verdict(false, av.ConsPercGaps);\r
+ ccs = new ConservationColourScheme(c, ccs.cs);\r
+\r
+ sg.cs = ccs;\r
+ }\r
+\r
+ av.alignment.addGroup(sg);\r
+ }\r
+ }\r
+ }\r
\r
- c.calculate();\r
- c.verdict(false, av.ConsPercGaps);\r
- ccs = new ConservationColourScheme(c, ccs.cs);\r
+ PaintRefresher.Refresh(this, av.alignment);\r
+ repaint();\r
+ }\r
\r
- sg.cs = ccs;\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param state DOCUMENT ME!\r
+ */\r
+ public void setShowDistances(boolean state)\r
+ {\r
+ this.showDistances = state;\r
+ repaint();\r
+ }\r
\r
- av.alignment.addGroup(sg);\r
- }\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param state DOCUMENT ME!\r
+ */\r
+ public void setShowBootstrap(boolean state)\r
+ {\r
+ this.showBootstrap = state;\r
+ repaint();\r
}\r
\r
- PaintRefresher.Refresh(this, av.alignment);\r
- repaint();\r
- }\r
-\r
- public void setShowDistances(boolean state)\r
- {\r
- this.showDistances = state;\r
- repaint();\r
- }\r
-\r
- public void setShowBootstrap(boolean state)\r
- {\r
- this.showBootstrap = state;\r
- repaint();\r
- }\r
-\r
- public void setMarkPlaceholders(boolean state)\r
- {\r
- this.markPlaceholders = state;\r
- repaint();\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param state DOCUMENT ME!\r
+ */\r
+ public void setMarkPlaceholders(boolean state)\r
+ {\r
+ this.markPlaceholders = state;\r
+ repaint();\r
+ }\r
}\r
git://source.jalview.org / jalview.git / blobdiff