/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 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
-*/
+ * 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!
*
public String annotationId;
- public SequenceI sequenceRef;
+ public SequenceI sequenceRef;
- /** DOCUMENT ME!! */
- public String label;
+ /** DOCUMENT ME!! */
+ public String label;
- /** DOCUMENT ME!! */
- public String description;
+ /** DOCUMENT ME!! */
+ public String description;
- /** DOCUMENT ME!! */
- public Annotation[] annotations;
+ /** DOCUMENT ME!! */
+ public Annotation[] annotations;
- public java.util.Hashtable sequenceMapping;
+ public java.util.Hashtable sequenceMapping;
- /** DOCUMENT ME!! */
- public float graphMin;
+ /** DOCUMENT ME!! */
+ public float graphMin;
- /** DOCUMENT ME!! */
- public float graphMax;
+ /** DOCUMENT ME!! */
+ public float graphMax;
- public GraphLine threshold;
+ public GraphLine threshold;
- // Graphical hints and tips
+ // Graphical hints and tips
- /** DOCUMENT ME!! */
- public boolean editable = false;
+ /** DOCUMENT ME!! */
+ public boolean editable = false;
- /** DOCUMENT ME!! */
- public boolean hasIcons; //
+ /** DOCUMENT ME!! */
+ public boolean hasIcons; //
- /** DOCUMENT ME!! */
- public boolean hasText;
+ /** DOCUMENT ME!! */
+ public boolean hasText;
- /** DOCUMENT ME!! */
- public boolean visible = true;
+ /** DOCUMENT ME!! */
+ public boolean visible = true;
- public int graphGroup = -1;
+ public int graphGroup = -1;
- /** DOCUMENT ME!! */
- public int height = 0;
+ /** DOCUMENT ME!! */
+ public int height = 0;
- public int graph = 0;
+ public int graph = 0;
- public int graphHeight = 40;
+ public int graphHeight = 40;
- public static final int NO_GRAPH = 0;
+ public static final int NO_GRAPH = 0;
- public static final int BAR_GRAPH = 1;
+ public static final int BAR_GRAPH = 1;
- public static final int LINE_GRAPH = 2;
+ public static final int LINE_GRAPH = 2;
- public static int getGraphValueFromString(String string)
+ public static int getGraphValueFromString(String string)
+ {
+ if (string.equalsIgnoreCase("BAR_GRAPH"))
{
- if(string.equalsIgnoreCase("BAR_GRAPH"))
- return BAR_GRAPH;
- else if(string.equalsIgnoreCase("LINE_GRAPH"))
- return LINE_GRAPH;
- else
- return NO_GRAPH;
+ return BAR_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)
+ else if (string.equalsIgnoreCase("LINE_GRAPH"))
{
- // always editable?
- editable = true;
- this.label = label;
- this.description = description;
- this.annotations = annotations;
-
- areLabelsSecondaryStructure();
+ return LINE_GRAPH;
}
-
- void areLabelsSecondaryStructure()
+ else
{
- boolean nonSSLabel = false;
- for (int i = 0; i < annotations.length; i++)
+ 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)
{
- if(annotations[i]==null)
- continue;
+ continue;
+ }
- if (annotations[i].secondaryStructure == 'H' ||
- annotations[i].secondaryStructure == 'E')
- {
- hasIcons = true;
- }
+ 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 (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)
{
- if(jalview.schemes.ResidueProperties.aaIndex
- [annotations[i].displayCharacter.charAt(0)]<23)
- {
- nonSSLabel = true;
- }
+ nonSSLabel = true;
}
+ }
- if (annotations[i].displayCharacter.length() > 0)
- {
- hasText = true;
- }
+ if (annotations[i].displayCharacter.length() > 0)
+ {
+ hasText = true;
}
+ }
- if(nonSSLabel)
+ if (nonSSLabel)
+ {
+ hasIcons = false;
+ for (int j = 0; j < annotations.length; j++)
{
- hasIcons = false;
- for (int j = 0; j < annotations.length; j++)
+ if (annotations[j] != null && annotations[j].secondaryStructure != ' ')
{
- if(annotations[j] !=null && annotations[j].secondaryStructure!=' ')
- {
- annotations[j].displayCharacter
- =String.valueOf(annotations[j].secondaryStructure);
- 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)
+ 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)
{
- // graphs are not editable
- this.label = label;
- this.description = description;
- this.annotations = annotations;
- graph = graphType;
+ min = 999999999;
+ for (int i = 0; i < annotations.length; i++)
+ {
+ if (annotations[i] == null)
+ {
+ continue;
+ }
- boolean drawValues = true;
+ if (drawValues && annotations[i].displayCharacter.length() > 1)
+ {
+ drawValues = false;
+ }
+
+ if (annotations[i].value > max)
+ {
+ max = annotations[i].value;
+ }
- if (min == max)
+ if (annotations[i].value < min)
{
- 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;
- }
- }
+ min = annotations[i].value;
}
+ }
+ }
- graphMin = min;
- graphMax = max;
+ graphMin = min;
+ graphMax = max;
- areLabelsSecondaryStructure();
+ areLabelsSecondaryStructure();
- if(!drawValues && graphType!=NO_GRAPH)
+ if (!drawValues && graphType != NO_GRAPH)
+ {
+ for (int i = 0; i < annotations.length; i++)
+ {
+ if (annotations[i] != null)
{
- for (int i = 0; i < annotations.length; i++)
- {
- if (annotations[i] != null)
- annotations[i].displayCharacter = "";
- }
+ annotations[i].displayCharacter = "";
}
+ }
}
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public String toString()
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String toString()
+ {
+ StringBuffer buffer = new StringBuffer();
+
+ for (int i = 0; i < annotations.length; i++)
{
- StringBuffer buffer = new StringBuffer();
-
- for (int i = 0; i < annotations.length; i++)
+ if (annotations[i] != null)
+ {
+ if (graph != 0)
{
- 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(", ");
+ buffer.append(annotations[i].value);
}
-
- if (label.equals("Consensus"))
+ else if (hasIcons)
{
- buffer.append("\n");
+ buffer.append(annotations[i].secondaryStructure);
+ }
+ else
+ {
+ buffer.append(annotations[i].displayCharacter);
+ }
+ }
+
+ buffer.append(", ");
+ }
- for (int i = 0; i < annotations.length; i++)
- {
- if (annotations[i] != null)
- {
- buffer.append(annotations[i].description);
- }
+ if (label.equals("Consensus"))
+ {
+ buffer.append("\n");
- buffer.append(", ");
- }
+ for (int i = 0; i < annotations.length; i++)
+ {
+ if (annotations[i] != null)
+ {
+ buffer.append(annotations[i].description);
}
- return buffer.toString();
+ buffer.append(", ");
}
+ }
- public void setThreshold(GraphLine line)
- {
- threshold = line;
- }
+ 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;
+ }
- public GraphLine getThreshold()
- {
- return threshold;
- }
+ sequenceMapping = new java.util.Hashtable();
+
+ sequenceRef = seqRef;
+ int seqPos;
- /**
- * 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)
+ for (int i = 0; i < annotations.length; i++)
+ {
+ if (annotations[i] != null)
{
+ if (alreadyMapped)
+ {
+ seqPos = seqRef.findPosition(i);
+ }
+ else
+ {
+ seqPos = i + startRes;
+ }
- if(seqRef == null)
- return;
+ sequenceMapping.put(new Integer(seqPos), annotations[i]);
+ }
+ }
+ }
- sequenceMapping = new java.util.Hashtable();
+ public void adjustForAlignment()
+ {
+ int a = 0, aSize = sequenceRef.getLength();
- sequenceRef = seqRef;
- int seqPos;
+ if (aSize == 0)
+ {
+ //Its been deleted
+ return;
+ }
- for(int i = 0; i < annotations.length; i++)
- {
- if (annotations[i] != null)
- {
- if(alreadyMapped)
- seqPos = seqRef.findPosition(i);
- else
- seqPos = i+startRes;
+ int position;
+ Annotation[] temp = new Annotation[aSize];
+ Integer index;
- sequenceMapping.put(new Integer(seqPos), annotations[i]);
- }
- }
+ 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);
}
+ }
- 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;
- }
+ annotations = temp;
+ }
}
-
-
git://source.jalview.org / jalview.git / blobdiff