JScrollPane scrollPane;\r
AlignViewport av;\r
Font font;\r
- int fontSize = 12;\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 = 20;\r
+ int offy;\r
float threshold;\r
String longestName;\r
int labelLength = -1;\r
* @param scroller DOCUMENT ME!\r
* @param label DOCUMENT ME!\r
*/\r
- public TreeCanvas(AlignViewport av, NJTree tree, JScrollPane scroller,\r
- String label)\r
+ public TreeCanvas(AlignViewport av, JScrollPane scroller)\r
{\r
this.av = av;\r
- this.tree = tree;\r
+ font = av.getFont();\r
scrollPane = scroller;\r
addMouseListener(this);\r
- tree.findHeight(tree.getTopNode());\r
- longestName = label;\r
-\r
PaintRefresher.Register(this, av.alignment);\r
}\r
\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
av.setSelectionGroup(selected);\r
}\r
\r
- selected.setEndRes(av.alignment.getWidth());\r
+ selected.setEndRes(av.alignment.getWidth()-1);\r
selected.addOrRemove(sequence, true);\r
\r
PaintRefresher.Refresh(this, av.alignment);\r
{\r
this.tree = tree;\r
tree.findHeight(tree.getTopNode());\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
+ if (longestName.length() < ( (Sequence) lf.element()).getName()\r
+ .length())\r
+ {\r
+ longestName = TreeCanvas.PLACEHOLDER +\r
+ ( (Sequence) lf.element()).getName();\r
+ }\r
+ }\r
+\r
+ setMarkPlaceholders(has_placeholders);\r
}\r
\r
/**\r
\r
String name = (markPlaceholders && node.isPlaceholder())\r
? (PLACEHOLDER + node.getName()) : node.getName();\r
- FontMetrics fm = g.getFontMetrics(font);\r
+\r
int charWidth = fm.stringWidth(name) + 3;\r
- int charHeight = fm.getHeight();\r
+ int charHeight = font.getSize();\r
\r
- Rectangle rect = new Rectangle(xend + 20, ypos - charHeight,\r
+ Rectangle rect = new Rectangle(xend+10, ypos-charHeight/2,\r
charWidth, charHeight);\r
\r
nameHash.put((SequenceI) node.element(), rect);\r
{\r
g.setColor(Color.gray);\r
\r
- g.fillRect(xend + 10, ypos - charHeight + 3, charWidth,\r
+ g.fillRect(xend + 10, ypos-charHeight/2, charWidth,\r
charHeight);\r
g.setColor(Color.white);\r
}\r
\r
- g.drawString(name, xend + 10, ypos);\r
+ g.drawString(name, xend + 10, ypos+fm.getDescent());\r
g.setColor(Color.black);\r
}\r
else\r
((SequenceNode) top.right()).count;\r
}\r
\r
- float chunk = (float) (height - (offy * 2)) / top.count;\r
+ float chunk = (float) (height - (offy)) / top.count;\r
\r
pickNode(pickBox, top, chunk, wscale, width, offx, offy);\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
\r
- FontMetrics fm = g.getFontMetrics(font);\r
-\r
- if (nameHash.size() == 0)\r
+ if(tree==null)\r
{\r
- repaint();\r
+ g.drawString("Calculating tree....", 20, getHeight()/2);\r
}\r
-\r
- if (fitToWindow ||\r
- (!fitToWindow &&\r
- (scrollPane.getHeight() > ((fm.getHeight() * nameHash.size()) +\r
- offy))))\r
+ else\r
{\r
+ fm = g.getFontMetrics(font);\r
+\r
+ if (nameHash.size() == 0)\r
+ {\r
+ repaint();\r
+ }\r
+\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
+ }\r
+ else\r
+ {\r
setPreferredSize(new Dimension(scrollPane.getWidth(),\r
- fm.getHeight() * nameHash.size()));\r
+ fm.getHeight() * nameHash.size()));\r
draw(g, scrollPane.getWidth(), fm.getHeight() * nameHash.size());\r
- }\r
+ }\r
\r
- scrollPane.revalidate();\r
+ scrollPane.revalidate();\r
+ }\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public int getFontSize()\r
- {\r
- return fontSize;\r
- }\r
\r
/**\r
* DOCUMENT ME!\r
*\r
* @param fontSize DOCUMENT ME!\r
*/\r
- public void setFontSize(int fontSize)\r
+ public void setFont(Font font)\r
{\r
- this.fontSize = fontSize;\r
+ this.font = font;\r
repaint();\r
}\r
\r
g2.setColor(Color.white);\r
g2.fillRect(0, 0, width, height);\r
\r
- labelLength = g2.getFontMetrics(font).stringWidth(longestName) + 20; //20 allows for scrollbar\r
+ g2.setFont(font);\r
+\r
+ offy = font.getSize()*2;\r
+\r
+ fm = g2.getFontMetrics(font);\r
+\r
+ labelLength = fm.stringWidth(longestName) + 20; //20 allows for scrollbar\r
\r
float wscale = (float) (width - labelLength - (offx * 2)) / tree.getMaxHeight();\r
\r
((SequenceNode) top.right()).count;\r
}\r
\r
- float chunk = (float) (height - (offy * 2)) / top.count;\r
+ float chunk = (float) (height - (offy)) / top.count;\r
\r
drawNode(g2, tree.getTopNode(), chunk, wscale, width, offx, offy);\r
\r
}\r
}\r
\r
- ColourSchemeI cs = ColourSchemeProperty.getColour(sequences,\r
- av.alignment.getWidth(),\r
- ColourSchemeProperty.getColourName(\r
- av.getGlobalColourScheme()));\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
- if (sg.cs != null)\r
- {\r
- sg.cs.setThreshold(25, av.getIgnoreGapsConsensus());\r
- }\r
\r
if ( av.getGlobalColourScheme()!=null\r
&& av.getGlobalColourScheme().conservationApplied())\r
git://source.jalview.org / jalview.git / blobdiff