- consensusV = alignment.getAAFrequency();\r
- StringBuffer sb = new StringBuffer();\r
- Hashtable hash = null;\r
- for (int i = 0; i < consensusV.size(); i++)\r
- {\r
- hash = (Hashtable) consensusV.elementAt(i);\r
- sb.append(hash.get("maxResidue").toString().charAt(0));\r
- }\r
- visibleConsensus = sb.toString();\r
- }\r
-\r
-\r
- return consensusV;\r
- }\r
-\r
-\r
- public SequenceGroup getSelectionGroup()\r
- {\r
- return selectionGroup;\r
- }\r
-\r
- public void setSelectionGroup(SequenceGroup sg)\r
- {\r
- selectionGroup = sg;\r
- }\r
-\r
-\r
- public boolean getConservationSelected()\r
- {\r
- return conservationColourSelected;\r
- }\r
-\r
- public void setConservationSelected(boolean b)\r
- {\r
- conservationColourSelected = b;\r
- }\r
-\r
- public boolean getAbovePIDThreshold()\r
- {\r
- return abovePIDThreshold;\r
- }\r
-\r
- public void setAbovePIDThreshold(boolean b)\r
- {\r
- abovePIDThreshold = b;\r
- }\r
-\r
- public int getStartRes() {\r
- return startRes;\r
- }\r
-\r
- public int getEndRes() {\r
- return endRes;\r
- }\r
-\r
- public int getStartSeq() {\r
- return startSeq;\r
- }\r
-\r
- public void setGlobalColourScheme(ColourSchemeI cs)\r
- {\r
- globalColourScheme = cs;\r
- }\r
-\r
- public ColourSchemeI getGlobalColourScheme()\r
- {\r
- return globalColourScheme;\r
- }\r
-\r
-\r
- public void setStartRes(int res) {\r
- this.startRes = res;\r
- }\r
- public void setStartSeq(int seq) {\r
- this.startSeq = seq;\r
- }\r
- public void setEndRes(int res) {\r
- if (res > alignment.getWidth()-1) {\r
- System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));\r
- res = alignment.getWidth() -1;\r
- }\r
- if (res < 0) {\r
- res = 0;\r
- }\r
- this.endRes = res;\r
- }\r
- public void setEndSeq(int seq) {\r
- if (seq > alignment.getHeight()) {\r
- seq = alignment.getHeight();\r
- }\r
- if (seq < 0) {\r
- seq = 0;\r
- }\r
- this.endSeq = seq;\r
- }\r
- public int getEndSeq() {\r
- return endSeq;\r
- }\r
-\r
- public void setFont(Font f) {\r
- font = f;\r
- javax.swing.JFrame temp = new javax.swing.JFrame();\r
- temp.addNotify();\r
- java.awt.FontMetrics fm = temp.getGraphics().getFontMetrics(font);\r
- setCharHeight(fm.getHeight());\r
- setCharWidth(fm.charWidth('M'));\r
- }\r
-\r
- public Font getFont() {\r
- return font;\r
- }\r
- public void setCharWidth(int w) {\r
- this.charWidth = w;\r
- }\r
- public int getCharWidth() {\r
- return charWidth;\r
- }\r
- public void setCharHeight(int h) {\r
- this.charHeight = h;\r
- }\r
- public int getCharHeight() {\r
- return charHeight;\r
- }\r
- public void setChunkWidth(int w) {\r
- this.chunkWidth = w;\r
- }\r
- public int getChunkWidth() {\r
- return chunkWidth;\r
- }\r
- public void setChunkHeight(int h) {\r
- this.chunkHeight = h;\r
- }\r
- public int getChunkHeight() {\r
- return chunkHeight;\r
- }\r
- public AlignmentI getAlignment() {\r
- return alignment;\r
- }\r
- public void setAlignment(AlignmentI align) {\r
- this.alignment = align;\r
- }\r
-\r
- public void setWrapAlignment(boolean state) {\r
- wrapAlignment = state;\r
- }\r
- public void setShowText(boolean state) {\r
- showText = state;\r
- }\r
-\r
- public void setRenderGaps(boolean state){\r
- renderGaps = state;\r
- if(renderer instanceof SequenceRenderer)\r
- {\r
- SequenceRenderer sr = (SequenceRenderer)renderer;\r
- sr.renderGaps(state);\r
- }\r
- }\r
-\r
-\r
- public boolean getColourText()\r
- {\r
- return showColourText;\r
- }\r
-\r
- public void setColourText(boolean state)\r
- {\r
- showColourText = state;\r
- }\r
-\r
- public void setShowBoxes(boolean state) {\r
- showBoxes = state;\r
- }\r
-\r
- public boolean getWrapAlignment() {\r
- return wrapAlignment;\r
- }\r
- public boolean getShowText() {\r
- return showText;\r
- }\r
- public boolean getShowBoxes() {\r
- return showBoxes;\r
- }\r
-\r
- public char getGapCharacter() {\r
- return getAlignment().getGapCharacter();\r
- }\r
- public void setGapCharacter(char gap) {\r
- if (getAlignment() != null) {\r
- getAlignment().setGapCharacter(gap);\r
- }\r
- }\r
- public void setThreshold(int thresh) {\r
- threshold = thresh;\r
- }\r
- public int getThreshold() {\r
- return threshold;\r
- }\r
- public void setIncrement(int inc) {\r
- increment = inc;\r
- }\r
- public int getIncrement() {\r
- return increment;\r
- }\r
- public int getIndex(int y) {\r
- int y1 = 0;\r
- int starty = getStartSeq();\r
- int endy = getEndSeq();\r
-\r
- for (int i = starty; i <= endy; i++) {\r
- if (i < alignment.getHeight() && alignment.getSequenceAt(i) != null) {\r
- int y2 = y1 + getCharHeight();\r
-\r
- if (y>=y1 && y <=y2) {\r
- return i;\r
+ return endSeq;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param f DOCUMENT ME!\r
+ */\r
+ public void setFont(Font f)\r
+ {\r
+ font = f;\r
+\r
+ Container c = new Container();\r
+\r
+ java.awt.FontMetrics fm = c.getFontMetrics(font);\r
+ setCharHeight(fm.getHeight());\r
+ setCharWidth(fm.charWidth('M'));\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public Font getFont()\r
+ {\r
+ return font;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param w DOCUMENT ME!\r
+ */\r
+ public void setCharWidth(int w)\r
+ {\r
+ this.charWidth = w;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public int getCharWidth()\r
+ {\r
+ return charWidth;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param h DOCUMENT ME!\r
+ */\r
+ public void setCharHeight(int h)\r
+ {\r
+ this.charHeight = h;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public int getCharHeight()\r
+ {\r
+ return charHeight;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param w DOCUMENT ME!\r
+ */\r
+ public void setWrappedWidth(int w)\r
+ {\r
+ this.wrappedWidth = w;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public int getWrappedWidth()\r
+ {\r
+ return wrappedWidth;\r
+ }\r
+\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public AlignmentI getAlignment()\r
+ {\r
+ return alignment;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param align DOCUMENT ME!\r
+ */\r
+ public void setAlignment(AlignmentI align)\r
+ {\r
+ this.alignment = align;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param state DOCUMENT ME!\r
+ */\r
+ public void setWrapAlignment(boolean state)\r
+ {\r
+ wrapAlignment = state;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param state DOCUMENT ME!\r
+ */\r
+ public void setShowText(boolean state)\r
+ {\r
+ showText = state;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param state DOCUMENT ME!\r
+ */\r
+ public void setRenderGaps(boolean state)\r
+ {\r
+ renderGaps = state;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public boolean getColourText()\r
+ {\r
+ return showColourText;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param state DOCUMENT ME!\r
+ */\r
+ public void setColourText(boolean state)\r
+ {\r
+ showColourText = state;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param state DOCUMENT ME!\r
+ */\r
+ public void setShowBoxes(boolean state)\r
+ {\r
+ showBoxes = state;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public boolean getWrapAlignment()\r
+ {\r
+ return wrapAlignment;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public boolean getShowText()\r
+ {\r
+ return showText;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public boolean getShowBoxes()\r
+ {\r
+ return showBoxes;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public char getGapCharacter()\r
+ {\r
+ return getAlignment().getGapCharacter();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param gap DOCUMENT ME!\r
+ */\r
+ public void setGapCharacter(char gap)\r
+ {\r
+ if (getAlignment() != null)\r
+ {\r
+ getAlignment().setGapCharacter(gap);\r