-/*\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 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(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) &&\r
- (annotations[i].displayCharacter.length() > 0))\r
- {\r
- hasText = true;\r
- }\r
- }\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
- * @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
- // 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(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
- 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
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ */
+package jalview.datamodel;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class AlignmentAnnotation
+{
+ /** If true, this annotations is calculated every edit,
+ * eg consensus, quality or conservation graphs */
+ public boolean autoCalculated = false;
+
+ public String annotationId;
+
+ public SequenceI sequenceRef;
+
+ /** DOCUMENT ME!! */
+ public String label;
+
+ /** DOCUMENT ME!! */
+ public String description;
+
+ /** DOCUMENT ME!! */
+ public Annotation[] annotations;
+
+ public java.util.Hashtable sequenceMapping;
+
+ /** DOCUMENT ME!! */
+ public float graphMin;
+
+ /** DOCUMENT ME!! */
+ public float graphMax;
+
+ public GraphLine threshold;
+
+ // Graphical hints and tips
+
+ /** DOCUMENT ME!! */
+ public boolean editable = false;
+
+ /** DOCUMENT ME!! */
+ public boolean hasIcons; //
+
+ /** DOCUMENT ME!! */
+ public boolean hasText;
+
+ /** DOCUMENT ME!! */
+ public boolean visible = true;
+
+ public int graphGroup = -1;
+
+ /** DOCUMENT ME!! */
+ public int height = 0;
+
+ public int graph = 0;
+
+ public int graphHeight = 40;
+
+ public static final int NO_GRAPH = 0;
+
+ public static final int BAR_GRAPH = 1;
+
+ public static final int LINE_GRAPH = 2;
+
+ public static int getGraphValueFromString(String string)
+ {
+ if (string.equalsIgnoreCase("BAR_GRAPH"))
+ {
+ return BAR_GRAPH;
+ }
+ else if (string.equalsIgnoreCase("LINE_GRAPH"))
+ {
+ return LINE_GRAPH;
+ }
+ else
+ {
+ return NO_GRAPH;
+ }
+ }
+
+ /**
+ * Creates a new AlignmentAnnotation object.
+ *
+ * @param label DOCUMENT ME!
+ * @param description DOCUMENT ME!
+ * @param annotations DOCUMENT ME!
+ */
+ public AlignmentAnnotation(String label, String description,
+ Annotation[] annotations)
+ {
+ // always editable?
+ editable = true;
+ this.label = label;
+ this.description = description;
+ this.annotations = annotations;
+
+ areLabelsSecondaryStructure();
+ }
+
+ void areLabelsSecondaryStructure()
+ {
+ boolean nonSSLabel = false;
+ for (int i = 0; i < annotations.length; i++)
+ {
+ if (annotations[i] == null)
+ {
+ continue;
+ }
+
+ if (annotations[i].secondaryStructure == 'H' ||
+ annotations[i].secondaryStructure == 'E')
+ {
+ hasIcons = true;
+ }
+
+ if (annotations[i].displayCharacter.length() == 1
+ && !annotations[i].displayCharacter.equals("H")
+ && !annotations[i].displayCharacter.equals("E")
+ && !annotations[i].displayCharacter.equals("-")
+ && !annotations[i].displayCharacter.equals("."))
+ {
+ if (jalview.schemes.ResidueProperties.aaIndex
+ [annotations[i].displayCharacter.charAt(0)] < 23)
+ {
+ nonSSLabel = true;
+ }
+ }
+
+ if (annotations[i].displayCharacter.length() > 0)
+ {
+ hasText = true;
+ }
+ }
+
+ if (nonSSLabel)
+ {
+ hasIcons = false;
+ for (int j = 0; j < annotations.length; j++)
+ {
+ if (annotations[j] != null && annotations[j].secondaryStructure != ' ')
+ {
+ annotations[j].displayCharacter
+ = String.valueOf(annotations[j].secondaryStructure);
+ annotations[j].secondaryStructure = ' ';
+ }
+
+ }
+
+ }
+
+ annotationId = this.hashCode() + "";
+ }
+
+ /**
+ * Creates a new AlignmentAnnotation object.
+ *
+ * @param label DOCUMENT ME!
+ * @param description DOCUMENT ME!
+ * @param annotations DOCUMENT ME!
+ * @param min DOCUMENT ME!
+ * @param max DOCUMENT ME!
+ * @param winLength DOCUMENT ME!
+ */
+ public AlignmentAnnotation(String label, String description,
+ Annotation[] annotations, float min, float max,
+ int graphType)
+ {
+ // graphs are not editable
+ this.label = label;
+ this.description = description;
+ this.annotations = annotations;
+ graph = graphType;
+
+ boolean drawValues = true;
+
+ if (min == max)
+ {
+ min = 999999999;
+ for (int i = 0; i < annotations.length; i++)
+ {
+ if (annotations[i] == null)
+ {
+ continue;
+ }
+
+ if (drawValues && annotations[i].displayCharacter.length() > 1)
+ {
+ drawValues = false;
+ }
+
+ if (annotations[i].value > max)
+ {
+ max = annotations[i].value;
+ }
+
+ if (annotations[i].value < min)
+ {
+ min = annotations[i].value;
+ }
+ }
+ }
+
+ graphMin = min;
+ graphMax = max;
+
+ areLabelsSecondaryStructure();
+
+ if (!drawValues && graphType != NO_GRAPH)
+ {
+ for (int i = 0; i < annotations.length; i++)
+ {
+ if (annotations[i] != null)
+ {
+ annotations[i].displayCharacter = "";
+ }
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String toString()
+ {
+ StringBuffer buffer = new StringBuffer();
+
+ for (int i = 0; i < annotations.length; i++)
+ {
+ if (annotations[i] != null)
+ {
+ if (graph != 0)
+ {
+ buffer.append(annotations[i].value);
+ }
+ else if (hasIcons)
+ {
+ buffer.append(annotations[i].secondaryStructure);
+ }
+ else
+ {
+ buffer.append(annotations[i].displayCharacter);
+ }
+ }
+
+ buffer.append(", ");
+ }
+
+ if (label.equals("Consensus"))
+ {
+ buffer.append("\n");
+
+ for (int i = 0; i < annotations.length; i++)
+ {
+ if (annotations[i] != null)
+ {
+ buffer.append(annotations[i].description);
+ }
+
+ buffer.append(", ");
+ }
+ }
+
+ return buffer.toString();
+ }
+
+ public void setThreshold(GraphLine line)
+ {
+ threshold = line;
+ }
+
+ public GraphLine getThreshold()
+ {
+ return threshold;
+ }
+
+ /**
+ * Attach the annotation to seqRef, starting from startRes position. If alreadyMapped is true then the indices of the annotation[] array are sequence positions rather than alignment column positions.
+ * @param seqRef
+ * @param startRes
+ * @param alreadyMapped
+ */
+ public void createSequenceMapping(SequenceI seqRef,
+ int startRes,
+ boolean alreadyMapped)
+ {
+
+ if (seqRef == null)
+ {
+ return;
+ }
+
+ sequenceMapping = new java.util.Hashtable();
+
+ sequenceRef = seqRef;
+ int seqPos;
+
+ for (int i = 0; i < annotations.length; i++)
+ {
+ if (annotations[i] != null)
+ {
+ if (alreadyMapped)
+ {
+ seqPos = seqRef.findPosition(i);
+ }
+ else
+ {
+ seqPos = i + startRes;
+ }
+
+ sequenceMapping.put(new Integer(seqPos), annotations[i]);
+ }
+ }
+
+ }
+
+ public void adjustForAlignment()
+ {
+ int a = 0, aSize = sequenceRef.getLength();
+
+ if (aSize == 0)
+ {
+ //Its been deleted
+ return;
+ }
+
+ int position;
+ Annotation[] temp = new Annotation[aSize];
+ Integer index;
+
+ for (a = sequenceRef.getStart(); a <= sequenceRef.getEnd(); a++)
+ {
+ index = new Integer(a);
+ if (sequenceMapping.containsKey(index))
+ {
+ position = sequenceRef.findIndex(a) - 1;
+
+ temp[position] = (Annotation) sequenceMapping.get(index);
+ }
+ }
+
+ annotations = temp;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff