+/*\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
-\r
import jalview.analysis.*;\r
+\r
import jalview.datamodel.*;\r
-import jalview.util.*;\r
+\r
import jalview.schemes.*;\r
-import javax.swing.*;\r
+\r
+import jalview.util.*;\r
+\r
import java.awt.*;\r
import java.awt.event.*;\r
-import java.util.*;\r
import java.awt.print.*;\r
\r
-public class TreeCanvas extends JPanel implements MouseListener, Runnable, Printable\r
-{\r
- NJTree tree;\r
- JScrollPane scrollPane;\r
- AlignViewport av;\r
-\r
- Font font;\r
- int fontSize = 12;\r
-\r
- boolean fitToWindow = true;\r
- boolean showDistances = false;\r
- boolean showBootstrap = false;\r
+import java.util.*;\r
\r
- int offx = 20;\r
- int offy = 20;\r
+import javax.swing.*;\r
\r
- float threshold;\r
\r
- String longestName;\r
- int labelLength=-1;\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
+ /** DOCUMENT ME!! */\r
+ public static final String PLACEHOLDER = " * ";\r
+ NJTree tree;\r
+ JScrollPane scrollPane;\r
+ AlignViewport av;\r
+ Font font;\r
+ FontMetrics fm;\r
+ boolean fitToWindow = true;\r
+ boolean showDistances = false;\r
+ boolean showBootstrap = false;\r
+ boolean markPlaceholders = false;\r
+ int offx = 20;\r
+ int offy;\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, JScrollPane scroller)\r
+ {\r
+ this.av = av;\r
+ font = av.getFont();\r
+ scrollPane = scroller;\r
+ addMouseListener(this);\r
+ PaintRefresher.Register(this, av.alignment);\r
+ }\r
\r
- //RubberbandRectangle rubberband;\r
\r
- Vector listeners;\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
- Hashtable nameHash = new Hashtable();\r
- Hashtable nodeHash = new Hashtable();\r
+ if (selected == null)\r
+ {\r
+ selected = new SequenceGroup();\r
+ av.setSelectionGroup(selected);\r
+ }\r
\r
- public TreeCanvas(AlignViewport av, NJTree tree, JScrollPane scroller, 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
+ selected.setEndRes(av.alignment.getWidth()-1);\r
+ selected.addOrRemove(sequence, true);\r
\r
- PaintRefresher.Register(this);\r
- }\r
- public void TreeSelectionChanged(Sequence sequence)\r
- {\r
- SequenceGroup selected = av.getSelectionGroup();\r
- if(selected == null)\r
- {\r
- selected = new SequenceGroup();\r
- av.setSelectionGroup(selected);\r
+ PaintRefresher.Refresh(this, av.alignment);\r
+ repaint();\r
}\r
\r
- selected.setEndRes(av.alignment.getWidth());\r
- selected.addOrRemove(sequence);\r
-\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param tree DOCUMENT ME!\r
+ */\r
+ public void setTree(NJTree tree)\r
+ {\r
+ this.tree = tree;\r
+ tree.findHeight(tree.getTopNode());\r
\r
- PaintRefresher.Refresh(this);\r
- repaint();\r
- }\r
+ // Now have to calculate longest name based on the leaves\r
+ Vector leaves = tree.findLeaves(tree.getTopNode(), new Vector());\r
+ boolean has_placeholders = false;\r
+ longestName = "";\r
\r
+ for (int i = 0; i < leaves.size(); i++)\r
+ {\r
+ SequenceNode lf = (SequenceNode) leaves.elementAt(i);\r
\r
+ if (lf.isPlaceholder())\r
+ {\r
+ has_placeholders = true;\r
+ }\r
\r
- public void setTree(NJTree tree) {\r
- this.tree = tree;\r
- tree.findHeight(tree.getTopNode());\r
- }\r
+ if (longestName.length() < ( (Sequence) lf.element()).getName()\r
+ .length())\r
+ {\r
+ longestName = TreeCanvas.PLACEHOLDER +\r
+ ( (Sequence) lf.element()).getName();\r
+ }\r
+ }\r
\r
- public void drawNode(Graphics g,SequenceNode node, float chunk, float scale, int width,int offx, int offy) {\r
- if (node == null) {\r
- return;\r
+ setMarkPlaceholders(has_placeholders);\r
}\r
\r
- if (node.left() == null && node.right() == null) {\r
- // Drawing leaf node\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
+ if (node == null)\r
+ {\r
+ return;\r
+ }\r
\r
- float height = node.height;\r
- float dist = node.dist;\r
+ if ((node.left() == null) && (node.right() == null))\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() == 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
- int xstart = (int)((height-dist)*scale) + offx;\r
- int xend = (int)(height*scale) + offx;\r
+ // Draw horizontal line\r
+ g.drawLine(xstart, ypos, xend, ypos);\r
\r
- int ypos = (int)(node.ycount * chunk) + offy;\r
+ String nodeLabel = "";\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
- g.setColor( ( (SequenceI) ( (SequenceNode) node).element()).getColor().\r
- darker());\r
+ if (showDistances && (node.dist > 0))\r
+ {\r
+ nodeLabel = new Format("%-.2f").form(node.dist);\r
+ }\r
\r
- }\r
- else\r
- g.setColor(Color.black);\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+2, ypos - 2);\r
+ }\r
\r
- // Draw horizontal line\r
- g.drawLine(xstart,ypos,xend,ypos);\r
+ String name = (markPlaceholders && node.isPlaceholder())\r
+ ? (PLACEHOLDER + node.getName()) : node.getName();\r
\r
- String nodeLabel = "";\r
- if (showDistances && node.dist > 0) {\r
- nodeLabel = new Format("%5.2f").form(node.dist);\r
- }\r
- if (showBootstrap) {\r
- if (showDistances) {\r
- nodeLabel = nodeLabel + " : ";\r
- }\r
- nodeLabel = nodeLabel + String.valueOf(node.getBootstrap());\r
- }\r
- if (! nodeLabel.equals("")) {\r
- g.drawString(nodeLabel,xstart,ypos - 10);\r
- }\r
+ int charWidth = fm.stringWidth(name) + 3;\r
+ int charHeight = font.getSize();\r
\r
- // Colour selected leaves differently\r
- String name = node.getName();\r
- FontMetrics fm = g.getFontMetrics(font);\r
- int charWidth = fm.stringWidth(node.getName()) + 3;\r
- int charHeight = fm.getHeight();\r
+ Rectangle rect = new Rectangle(xend+10, ypos-charHeight/2,\r
+ charWidth, charHeight);\r
\r
- Rectangle rect = new Rectangle(xend+20,ypos-charHeight,\r
- charWidth,charHeight);\r
+ nameHash.put((SequenceI) node.element(), rect);\r
\r
- nameHash.put((SequenceI)node.element(),rect);\r
+ // Colour selected leaves differently\r
+ SequenceGroup selected = av.getSelectionGroup();\r
\r
- SequenceGroup selected = av.getSelectionGroup();\r
- if (selected!=null && selected.sequences.contains((SequenceI)node.element())) {\r
- g.setColor(Color.gray);\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,charHeight);\r
- g.setColor(Color.white);\r
- }\r
- g.drawString(node.getName(),xend+10,ypos);\r
- g.setColor(Color.black);\r
- } else {\r
- drawNode(g,(SequenceNode)node.left(), chunk,scale,width,offx,offy);\r
- drawNode(g,(SequenceNode)node.right(),chunk,scale,width,offx,offy);\r
+ g.fillRect(xend + 10, ypos-charHeight/2, charWidth,\r
+ charHeight);\r
+ g.setColor(Color.white);\r
+ }\r
\r
- float height = node.height;\r
- float dist = node.dist;\r
+ g.drawString(name, xend + 10, ypos+fm.getDescent());\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
- int xstart = (int)((height-dist)*scale) + offx;\r
- int xend = (int)(height *scale) + offx;\r
- int ypos = (int)(node.ycount *chunk) + offy;\r
+ float height = node.height;\r
+ float dist = node.dist;\r
\r
- g.setColor(((SequenceNode)node).color.darker());\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
- // Draw horizontal line\r
- g.drawLine(xstart,ypos,xend,ypos);\r
- g.fillRect(xend-2, ypos-2, 4,4);\r
+ g.setColor(((SequenceNode) node).color.darker());\r
\r
- int ystart = (int)(((SequenceNode)node.left()) .ycount * chunk) + offy;\r
- int yend = (int)(((SequenceNode)node.right()).ycount * chunk) + offy;\r
+ // Draw horizontal line\r
+ g.drawLine(xstart, ypos, xend, ypos);\r
+ g.fillRect(xend - 2, ypos - 2, 4, 4);\r
\r
- Rectangle pos = new Rectangle(xend-2,ypos-2,5,5);\r
- nodeHash.put(node,pos);\r
+ int ystart = (int) (((SequenceNode) node.left()).ycount * chunk) +\r
+ offy;\r
+ int yend = (int) (((SequenceNode) node.right()).ycount * chunk) +\r
+ offy;\r
\r
- g.drawLine((int)(height*scale) + offx, ystart,\r
- (int)(height*scale) + offx, yend);\r
+ Rectangle pos = new Rectangle(xend - 2, ypos - 2, 5, 5);\r
+ nodeHash.put(node, pos);\r
\r
- if (showDistances && node.dist > 0) {\r
- g.drawString(new Format("%5.2f").form(node.dist),xstart,ypos - 5);\r
- }\r
+ g.drawLine((int) (height * scale) + offx, ystart,\r
+ (int) (height * scale) + offx, yend);\r
\r
+ if (showDistances && (node.dist > 0))\r
+ {\r
+ g.drawString(new Format("%-.2f").form(node.dist).trim(), xstart+2,\r
+ ypos - 2);\r
+ }\r
+ }\r
}\r
- }\r
- public Object findElement(int x, int y) {\r
- Enumeration keys = nameHash.keys();\r
\r
- while (keys.hasMoreElements()) {\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
+ while (keys.hasMoreElements())\r
+ {\r
Object ob = keys.nextElement();\r
- Rectangle rect = (Rectangle)nameHash.get(ob);\r
+ Rectangle rect = (Rectangle) nameHash.get(ob);\r
\r
- if (x >= rect.x && x <= (rect.x + rect.width) &&\r
- y >= rect.y && y <= (rect.y + rect.height)) {\r
- return ob;\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
- keys = nodeHash.keys();\r
+ }\r
+\r
+ keys = nodeHash.keys();\r
\r
- while (keys.hasMoreElements()) {\r
+ while (keys.hasMoreElements())\r
+ {\r
Object ob = keys.nextElement();\r
- Rectangle rect = (Rectangle)nodeHash.get(ob);\r
+ Rectangle rect = (Rectangle) nodeHash.get(ob);\r
\r
- if (x >= rect.x && x <= (rect.x + rect.width) &&\r
- y >= rect.y && y <= (rect.y + rect.height)) {\r
- return ob;\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
+ return null;\r
}\r
- return null;\r
\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param pickBox DOCUMENT ME!\r
+ */\r
+ public void pickNodes(Rectangle pickBox)\r
+ {\r
+ int width = getWidth();\r
+ int height = getHeight();\r
+\r
+ SequenceNode top = tree.getTopNode();\r
+\r
+ float wscale = (float) ((width * .8) - (offx * 2)) / tree.getMaxHeight();\r
\r
- public void pickNodes(Rectangle pickBox) {\r
- int width = getWidth();\r
- int height = getHeight();\r
+ if (top.count == 0)\r
+ {\r
+ top.count = ((SequenceNode) top.left()).count +\r
+ ((SequenceNode) top.right()).count;\r
+ }\r
\r
- SequenceNode top = tree.getTopNode();\r
+ float chunk = (float) (height - (offy)) / top.count;\r
\r
- float wscale = (float)(width*.8-offx*2)/tree.getMaxHeight()\r
-;\r
- if (top.count == 0) {\r
- top.count = ((SequenceNode)top.left()).count + ((SequenceNode)top.right()).count ;\r
+ pickNode(pickBox, top, chunk, wscale, width, offx, offy);\r
}\r
- float chunk = (float)(height-offy*2)/top.count;\r
\r
- pickNode(pickBox,top,chunk,wscale,width,offx,offy);\r
- }\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
+ if (node == null)\r
+ {\r
+ return;\r
+ }\r
\r
- public void pickNode(Rectangle pickBox, SequenceNode node, float chunk, float scale, int width,int offx, int offy) {\r
- if (node == null) {\r
- return;\r
- }\r
+ if ((node.left() == null) && (node.right() == null))\r
+ {\r
+ float height = node.height;\r
+ float dist = node.dist;\r
\r
- if (node.left() == null && node.right() == null) {\r
- float height = node.height;\r
- float dist = node.dist;\r
+ int xstart = (int) ((height - dist) * scale) + offx;\r
+ int xend = (int) (height * scale) + offx;\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
- int ypos = (int)(node.ycount * chunk) + offy;\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 (pickBox.contains(new Point(xend,ypos))) {\r
- if (node.element() instanceof SequenceI) {\r
- SequenceI seq = (SequenceI)node.element();\r
- SequenceGroup sg = av.getSelectionGroup();\r
- if(sg!=null)\r
- sg.addOrRemove(seq);\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
- } else {\r
- pickNode(pickBox,(SequenceNode)node.left(), chunk,scale,width,offx,offy);\r
- pickNode(pickBox,(SequenceNode)node.right(),chunk,scale,width,offx,offy);\r
}\r
- }\r
\r
- public void setColor(SequenceNode node, Color c)\r
- {\r
- if (node == null)\r
- return;\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
- node.color = c;\r
+ if (node == null)\r
+ {\r
+ return;\r
+ }\r
\r
- if (node.element() instanceof SequenceI)\r
- ((SequenceI)node.element()).setColor(c);\r
- } else\r
- {\r
- node.color = c;\r
- setColor((SequenceNode)node.left(),c);\r
- setColor((SequenceNode)node.right(),c);\r
+ if ((node.left() == null) && (node.right() == null))\r
+ {\r
+ node.color = c;\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
-\r
- void startPrinting()\r
- {\r
- Thread thread = new Thread(this);\r
- thread.start();\r
- }\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
- printJob.setPrintable(this, pf);\r
- if (printJob.printDialog())\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
+ void startPrinting()\r
{\r
- try\r
- {\r
- printJob.print();\r
- }\r
- catch (Exception PrintException)\r
- {\r
- PrintException.printStackTrace();\r
- }\r
+ Thread thread = new Thread(this);\r
+ thread.start();\r
}\r
- }\r
-\r
-\r
- public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException\r
- {\r
- pg.setFont(font);\r
- FontMetrics fm = pg.getFontMetrics(font);\r
-\r
- pg.translate((int)pf.getImageableX(), (int)pf.getImageableY());\r
\r
- int pwidth = (int) pf.getImageableWidth();\r
- int pheight = (int) pf.getImageableHeight();\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
\r
- // adjust pheight to row height\r
- pheight -= (pheight%fm.getHeight());\r
- pg.setClip(0,0, pwidth, pheight);\r
+ printJob.setPrintable(this, pf);\r
\r
- int noPages = (fm.getHeight() * nameHash.size()) / pheight;\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
- if(pi>noPages)\r
- return Printable.NO_SUCH_PAGE;\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
- pg.translate(0, -pheight*pi );\r
- draw(pg, pwidth, fm.getHeight() * nameHash.size());\r
+ int pwidth = (int) pf.getImageableWidth();\r
+ int pheight = (int) pf.getImageableHeight();\r
\r
- return Printable.PAGE_EXISTS;\r
+ int noPages = getHeight() / pheight;\r
\r
- }\r
+ if (pi > noPages)\r
+ {\r
+ return Printable.NO_SUCH_PAGE;\r
+ }\r
\r
- public void paintComponent(Graphics g)\r
- {\r
+ if (pwidth > getWidth())\r
+ {\r
+ pwidth = getWidth();\r
+ }\r
\r
- font = new Font("Verdana",Font.PLAIN,fontSize);\r
- g.setFont(font);\r
+ if (fitToWindow)\r
+ {\r
+ if (pheight > getHeight())\r
+ {\r
+ pheight = getHeight();\r
+ }\r
\r
- FontMetrics fm = g.getFontMetrics(font);\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(nameHash.size()==0)\r
- repaint();\r
+ draw(pg, pwidth, pheight);\r
\r
+ return Printable.PAGE_EXISTS;\r
+ }\r
\r
- if( fitToWindow || (!fitToWindow && scrollPane.getHeight() > fm.getHeight() * nameHash.size()+offy ) )\r
- {\r
- draw(g,scrollPane.getWidth(),scrollPane.getHeight());\r
- setPreferredSize(null);\r
- }\r
- else\r
- {\r
- setPreferredSize(new Dimension(scrollPane.getWidth(), fm.getHeight() * nameHash.size()));\r
- draw( g,scrollPane.getWidth(), fm.getHeight() * nameHash.size());\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param g DOCUMENT ME!\r
+ */\r
+ public void paintComponent(Graphics g)\r
+ {\r
+ super.paintComponent(g);\r
+ g.setFont(font);\r
\r
+ if(tree==null)\r
+ {\r
+ g.drawString("Calculating tree....", 20, getHeight()/2);\r
+ }\r
+ else\r
+ {\r
+ fm = g.getFontMetrics(font);\r
\r
- if (threshold != 0)\r
- {\r
- g.setColor(Color.red);\r
+ if (nameHash.size() == 0)\r
+ {\r
+ repaint();\r
+ }\r
\r
- int x = (int)( threshold * (float)(getWidth()-labelLength - 2*offx) +offx ) ;\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
- g.drawLine(x,0,x,getHeight());\r
+ scrollPane.revalidate();\r
+ }\r
}\r
\r
- scrollPane.revalidate();\r
- }\r
- public int getFontSize() {\r
- return fontSize;\r
- }\r
- public void setFontSize(int fontSize) {\r
- this.fontSize = fontSize;\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param fontSize DOCUMENT ME!\r
+ */\r
+ public void setFont(Font font)\r
+ {\r
+ this.font = font;\r
repaint();\r
}\r
- public void draw(Graphics g, int width, int height) {\r
- g.setColor(Color.white);\r
- g.fillRect(0,0,width,height);\r
-\r
-\r
- labelLength = g.getFontMetrics(font).stringWidth(longestName)+ 20;//20 allows for scrollbar\r
-\r
- float wscale =(float)(width - labelLength -offx*2)/tree.getMaxHeight();\r
-\r
- SequenceNode top = tree.getTopNode();\r
\r
- if (top.count == 0) {\r
- top.count = ((SequenceNode)top.left()).count + ((SequenceNode)top.right()).count ;\r
- }\r
- float chunk = (float)(height-offy*2)/top.count ;\r
-\r
- drawNode(g,tree.getTopNode(),chunk,wscale,width,offx,offy);\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
+ 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
- public void mouseReleased(MouseEvent e) { }\r
- public void mouseEntered(MouseEvent e) { }\r
- public void mouseExited(MouseEvent e) { }\r
- public void mouseClicked(MouseEvent e) {\r
- }\r
+ g2.setFont(font);\r
\r
- public void mousePressed(MouseEvent e) {\r
- int x = e.getX();\r
- int y = e.getY();\r
+ offy = font.getSize()+10;\r
\r
- Object ob = findElement(x,y);\r
+ fm = g2.getFontMetrics(font);\r
\r
- if (ob instanceof SequenceI)\r
- {\r
- TreeSelectionChanged((Sequence)ob);\r
- repaint();\r
- return;\r
+ labelLength = fm.stringWidth(longestName) + 20; //20 allows for scrollbar\r
\r
- } else if (ob instanceof SequenceNode) {\r
- SequenceNode tmpnode = (SequenceNode)ob;\r
- tree.swapNodes(tmpnode);\r
- tree.reCount(tree.getTopNode());\r
- tree.findHeight(tree.getTopNode());\r
- } else {\r
- // Find threshold\r
+ float wscale = (float) (width - labelLength - (offx * 2)) / tree.getMaxHeight();\r
\r
- if (tree.getMaxHeight() != 0) {\r
- threshold = (float)(x - offx)/(float)(getWidth()-labelLength - 2*offx);\r
+ SequenceNode top = tree.getTopNode();\r
\r
- tree.getGroups().removeAllElements();\r
- tree.groupNodes(tree.getTopNode(),threshold);\r
- setColor(tree.getTopNode(),Color.black);\r
+ if (top.count == 0)\r
+ {\r
+ top.count = ((SequenceNode) top.left()).count +\r
+ ((SequenceNode) top.right()).count;\r
+ }\r
\r
- av.setSelectionGroup(null);\r
- av.alignment.deleteAllGroups();\r
+ float chunk = (float) (height - (offy)) / top.count;\r
\r
- for (int i=0; i < tree.getGroups().size(); i++)\r
- {\r
+ drawNode(g2, tree.getTopNode(), chunk, wscale, width, offx, offy);\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),col.brighter());\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
- Vector l = tree.findLeaves((SequenceNode)tree.getGroups().elementAt(i),new Vector());\r
- SequenceGroup sg = null;\r
- for (int j = 0; j < l.size(); j++)\r
- {\r
- SequenceNode sn = (SequenceNode) l.elementAt(j);\r
- if(sg==null)\r
- sg = new SequenceGroup("TreeGroup", av.getGlobalColourScheme(), true, true,false,0,av.alignment.getWidth());\r
+ int x = (int) ((threshold * (float) (getWidth() - labelLength -\r
+ (2 * offx))) + offx);\r
\r
- sg.addSequence( (Sequence) sn.element());\r
- }\r
+ g2.drawLine(x, 0, x, getHeight());\r
+ }\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,\r
- sg.sequences, sg.getStartRes(),\r
- sg.getEndRes());\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void mouseReleased(MouseEvent e)\r
+ {\r
+ }\r
\r
- c.calculate();\r
- c.verdict(false, 100);\r
- ccs = new ConservationColourScheme(c, ccs.cs);\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void mouseEntered(MouseEvent e)\r
+ {\r
+ }\r
\r
- sg.cs = ccs;\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void mouseExited(MouseEvent e)\r
+ {\r
+ }\r
\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void mouseClicked(MouseEvent e)\r
+ {\r
+ }\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\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
- av.alignment.addGroup(sg);\r
+ Object ob = findElement(x, y);\r
\r
- }\r
- }\r
- }\r
+ if (ob instanceof SequenceI)\r
+ {\r
+ TreeSelectionChanged((Sequence) ob);\r
+ repaint();\r
\r
- PaintRefresher.Refresh(this);\r
- repaint();\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 = null;\r
+\r
+ if (av.getGlobalColourScheme() != null)\r
+ {\r
+ if (av.getGlobalColourScheme() instanceof UserColourScheme)\r
+ {\r
+ cs = new UserColourScheme(\r
+ ( (UserColourScheme) av.getGlobalColourScheme()).getColours());\r
+\r
+ }\r
+ else\r
+ cs = ColourSchemeProperty.getColour(sequences,\r
+ av.alignment.getWidth(),\r
+ ColourSchemeProperty.getColourName(\r
+ av.getGlobalColourScheme()));\r
+\r
+ cs.setThreshold(av.getGlobalColourScheme().getThreshold(),\r
+ av.getIgnoreGapsConsensus());\r
+ }\r
+\r
+\r
+ SequenceGroup sg = new SequenceGroup(sequences,\r
+ "TreeGroup", cs, true, true, false, 0,\r
+ av.alignment.getWidth());\r
+\r
+\r
+ if ( av.getGlobalColourScheme()!=null\r
+ && av.getGlobalColourScheme().conservationApplied())\r
+ {\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
+ sg.cs.setConservation(c);\r
+ }\r
+\r
+ av.alignment.addGroup(sg);\r
+ }\r
+ }\r
+ }\r
\r
- }\r
+ PaintRefresher.Refresh(this, av.alignment);\r
+ repaint();\r
+ }\r
\r
- public void setShowDistances(boolean state) {\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
- public void setShowBootstrap(boolean state) {\r
- this.showBootstrap = state;\r
- repaint();\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
+ /**\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
-\r
git://source.jalview.org / jalview.git / blobdiff