+/*\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.datamodel;\r
\r
+\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
public class AlignmentAnnotation\r
{\r
- public String label;\r
- public String description;\r
- public Annotation [] annotations;\r
- public boolean isGraph = false;\r
- public float graphMin, graphMax;\r
- public int windowLength;\r
-\r
- // Graphical hints and tips\r
- public boolean editable = false;\r
- public boolean hasIcons; //\r
- public boolean hasText;\r
- public boolean visible = true;\r
- public int height=0;\r
-\r
- public AlignmentAnnotation(String label, String description, Annotation [] annotations)\r
- {\r
- // always editable?\r
- editable = true;\r
- this.label = label;\r
- this.description = description;\r
- this.annotations = annotations;\r
- for(int i=0; i<annotations.length; i++)\r
+ public SequenceI sequenceRef;\r
+\r
+ /** DOCUMENT ME!! */\r
+ public String label;\r
+\r
+ /** DOCUMENT ME!! */\r
+ public String description;\r
+\r
+ /** DOCUMENT ME!! */\r
+ public Annotation[] annotations;\r
+\r
+ public java.util.Hashtable sequenceMapping;\r
+\r
+ /** DOCUMENT ME!! */\r
+ public float graphMin;\r
+\r
+ /** DOCUMENT ME!! */\r
+ public float graphMax;\r
+\r
+ public GraphLine threshold;\r
+\r
+ // Graphical hints and tips\r
+\r
+ /** DOCUMENT ME!! */\r
+ public boolean editable = false;\r
+\r
+ /** DOCUMENT ME!! */\r
+ public boolean hasIcons; //\r
+\r
+ /** DOCUMENT ME!! */\r
+ public boolean hasText;\r
+\r
+ /** DOCUMENT ME!! */\r
+ public boolean visible = true;\r
+\r
+ public int graphGroup = -1;\r
+\r
+ /** DOCUMENT ME!! */\r
+ public int height = 0;\r
+\r
+ public int graph = 0;\r
+\r
+ public int graphHeight = 40;\r
+\r
+ public static final int NO_GRAPH = 0;\r
+\r
+ public static final int BAR_GRAPH = 1;\r
+\r
+ public static final int LINE_GRAPH = 2;\r
+\r
+ public static int getGraphValueFromString(String string)\r
{\r
- if (annotations[i]!=null &&(\r
- annotations[i].secondaryStructure == 'H' ||\r
- annotations[i].secondaryStructure == 'E'))\r
- hasIcons = true;\r
+ if(string.equalsIgnoreCase("BAR_GRAPH"))\r
+ return BAR_GRAPH;\r
+ else if(string.equalsIgnoreCase("LINE_GRAPH"))\r
+ return LINE_GRAPH;\r
+ else\r
+ return NO_GRAPH;\r
+ }\r
+\r
+ /**\r
+ * Creates a new AlignmentAnnotation object.\r
+ *\r
+ * @param label DOCUMENT ME!\r
+ * @param description DOCUMENT ME!\r
+ * @param annotations DOCUMENT ME!\r
+ */\r
+ public AlignmentAnnotation(String label, String description,\r
+ Annotation[] annotations)\r
+ {\r
+ // always editable?\r
+ editable = true;\r
+ this.label = label;\r
+ this.description = description;\r
+ this.annotations = annotations;\r
+\r
+ for (int i = 0; i < annotations.length; i++)\r
+ {\r
+ if ((annotations[i] != null) &&\r
+ ((annotations[i].secondaryStructure == 'H') ||\r
+ (annotations[i].secondaryStructure == 'E')))\r
+ {\r
+ hasIcons = true;\r
+ }\r
\r
- if (annotations[i]!=null && annotations[i].displayCharacter.length()>0)\r
- hasText = true;\r
+ if ((annotations[i] != null) &&\r
+ (annotations[i].displayCharacter.length() > 0))\r
+ {\r
+ hasText = true;\r
+ }\r
+ }\r
}\r
- }\r
-\r
- public AlignmentAnnotation(String label, String description, Annotation [] annotations, float min, float max, int winLength)\r
- {\r
- // graphs are not editable\r
- this.label = label;\r
- this.description = description;\r
- this.annotations = annotations;\r
- isGraph = true;\r
- graphMin = min;\r
- graphMax = max;\r
- windowLength = winLength;\r
- for(int i=0; i<annotations.length; i++)\r
+\r
+ /**\r
+ * Creates a new AlignmentAnnotation object.\r
+ *\r
+ * @param label DOCUMENT ME!\r
+ * @param description DOCUMENT ME!\r
+ * @param annotations DOCUMENT ME!\r
+ * @param min DOCUMENT ME!\r
+ * @param max DOCUMENT ME!\r
+ * @param winLength DOCUMENT ME!\r
+ */\r
+ public AlignmentAnnotation(String label, String description,\r
+ Annotation[] annotations, float min, float max, int graphType)\r
{\r
- if (annotations[i]!=null &&(\r
- annotations[i].secondaryStructure == 'H' ||\r
- annotations[i].secondaryStructure == 'E'))\r
- hasIcons = true;\r
+ // graphs are not editable\r
+ this.label = label;\r
+ this.description = description;\r
+ this.annotations = annotations;\r
+ graph = graphType;\r
+\r
+ boolean drawValues = true;\r
+\r
+ if (min == max)\r
+ {\r
+ min = 999999999;\r
+ for (int i = 0; i < annotations.length; i++)\r
+ {\r
+ if (annotations[i] == null)\r
+ {\r
+ continue;\r
+ }\r
\r
- if (annotations[i]!=null && annotations[i].displayCharacter.length()>0)\r
- hasText = true;\r
+ if(drawValues && annotations[i].displayCharacter.length() > 1 )\r
+ {\r
+ drawValues = false;\r
+ }\r
+\r
+ if (annotations[i].value > max)\r
+ {\r
+ max = annotations[i].value;\r
+ }\r
+\r
+ if (annotations[i].value < min)\r
+ {\r
+ min = annotations[i].value;\r
+ }\r
+ }\r
+ }\r
+\r
+ if(!drawValues)\r
+ {\r
+ for (int i = 0; i < annotations.length; i++)\r
+ {\r
+ if (annotations[i] != null)\r
+ annotations[i].displayCharacter = "";\r
+ }\r
+ }\r
+\r
+ graphMin = min;\r
+ graphMax = max;\r
+\r
+ for (int i = 0; i < annotations.length; i++)\r
+ {\r
+ if ((annotations[i] != null) &&\r
+ ((annotations[i].secondaryStructure == 'H') ||\r
+ (annotations[i].secondaryStructure == 'E')))\r
+ {\r
+ hasIcons = true;\r
+ }\r
+\r
+ if ((annotations[i] != null) &&\r
+ (annotations[i].displayCharacter.length() > 0))\r
+ {\r
+ hasText = true;\r
+ }\r
+ }\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public String toString()\r
+ {\r
+ StringBuffer buffer = new StringBuffer();\r
+\r
+ for (int i = 0; i < annotations.length; i++)\r
+ {\r
+ if (annotations[i] != null)\r
+ {\r
+ if (graph!=0)\r
+ {\r
+ buffer.append(annotations[i].value);\r
+ }\r
+ else if (hasIcons)\r
+ {\r
+ buffer.append(annotations[i].secondaryStructure);\r
+ }\r
+ else\r
+ {\r
+ buffer.append(annotations[i].displayCharacter);\r
+ }\r
+ }\r
+\r
+ buffer.append(", ");\r
+ }\r
+\r
+ if (label.equals("Consensus"))\r
+ {\r
+ buffer.append("\n");\r
+\r
+ for (int i = 0; i < annotations.length; i++)\r
+ {\r
+ if (annotations[i] != null)\r
+ {\r
+ buffer.append(annotations[i].description);\r
+ }\r
+\r
+ buffer.append(", ");\r
+ }\r
+ }\r
+\r
+ return buffer.toString();\r
+ }\r
+\r
+ public void setThreshold(GraphLine line)\r
+ {\r
+ threshold = line;\r
+ }\r
\r
- }\r
+ public GraphLine getThreshold()\r
+ {\r
+ return threshold;\r
+ }\r
\r
+ /**\r
+ * This\r
+ */\r
+ public void createSequenceMapping(SequenceI seqRef, int startRes)\r
+ {\r
+ if(seqRef == null)\r
+ return;\r
+\r
+ sequenceMapping = new java.util.Hashtable();\r
+\r
+ sequenceRef = seqRef;\r
+\r
+ if(startRes < sequenceRef.getStart())\r
+ startRes = sequenceRef.getStart();\r
+\r
+ int seqPos;\r
+\r
+ int fileOffset = 0;\r
+ if(startRes > sequenceRef.getStart())\r
+ {\r
+ fileOffset = startRes - sequenceRef.getStart();\r
+ }\r
+\r
+ for(int i = 0; i < annotations.length; i++)\r
+ {\r
+ seqPos = sequenceRef.findPosition(i + fileOffset);\r
+ if(seqPos<annotations.length)\r
+ {\r
+ if (annotations[i] != null)\r
+ {\r
+ sequenceMapping.put(new Integer(seqPos),\r
+ annotations[i]);\r
+ }\r
+ }\r
+ }\r
+\r
+ adjustForAlignment();\r
+\r
+ }\r
+\r
+ public void adjustForAlignment()\r
+ {\r
+ int a=0, aSize = sequenceRef.getLength();\r
+\r
+ int position;\r
+ Annotation[] temp = new Annotation[aSize];\r
+ Integer index;\r
+ for (a = sequenceRef.getStart(); a <= sequenceRef.getEnd(); a++)\r
+ {\r
+ index = new Integer(a);\r
+ if(sequenceMapping.containsKey(index))\r
+ {\r
+ position = sequenceRef.findIndex(a)-1;\r
+\r
+ temp[position] = (Annotation)sequenceMapping.get(index);\r
+ }\r
+ }\r
+\r
+ annotations = temp;\r
+ }\r
}\r
+\r
+\r
git://source.jalview.org / jalview.git / blobdiff