X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=ae81a90cf28e631113a8c975324ccd5c5ff267dd;hb=b7620d52027f3bb6f8bc7673563ea30a6adacf22;hp=c675a759bb71fe620a4fd7e5c2bf4f939b9f9e22;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java index c675a75..ae81a90 100755 --- a/src/jalview/datamodel/AlignmentAnnotation.java +++ b/src/jalview/datamodel/AlignmentAnnotation.java @@ -18,6 +18,9 @@ */ package jalview.datamodel; +import java.util.Enumeration; +import java.util.Hashtable; + /** * DOCUMENT ME! * @@ -51,6 +54,15 @@ public class AlignmentAnnotation /** DOCUMENT ME!! */ public float graphMax; + /** + * Score associated with label and description. + */ + public double score= Double.NaN; + /** + * flag indicating if annotation has a score. + */ + public boolean hasScore=false; + public GraphLine threshold; // Graphical hints and tips @@ -76,12 +88,17 @@ public class AlignmentAnnotation public int graphHeight = 40; + public boolean padGaps = true; + public static final int NO_GRAPH = 0; public static final int BAR_GRAPH = 1; public static final int LINE_GRAPH = 2; + public boolean belowAlignment = true; + + public static int getGraphValueFromString(String string) { if (string.equalsIgnoreCase("BAR_GRAPH")) @@ -103,7 +120,8 @@ public class AlignmentAnnotation * * @param label DOCUMENT ME! * @param description DOCUMENT ME! - * @param annotations DOCUMENT ME! + * @param annotations DOCUMENT ME!about:blank +Loading... */ public AlignmentAnnotation(String label, String description, Annotation[] annotations) @@ -114,7 +132,7 @@ public class AlignmentAnnotation this.description = description; this.annotations = annotations; - areLabelsSecondaryStructure(); + validateRangeAndDisplay(); } void areLabelsSecondaryStructure() @@ -124,13 +142,19 @@ public class AlignmentAnnotation { if (annotations[i] == null) { + padGaps = false; continue; } - if (annotations[i].secondaryStructure == 'H' || annotations[i].secondaryStructure == 'E') { - hasIcons = true; + hasIcons = true; + } + + if(annotations[i].displayCharacter==null) + { + padGaps = false; + continue; } if (annotations[i].displayCharacter.length() == 1 @@ -138,19 +162,21 @@ public class AlignmentAnnotation && !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 (jalview.schemes.ResidueProperties.aaIndex + [annotations[i].displayCharacter.charAt(0)] < 23) + { + nonSSLabel = true; + } } - } - if (annotations[i].displayCharacter.length() > 0) - { - hasText = true; + if (annotations[i].displayCharacter.length() > 0) + { + hasText = true; + } + else + padGaps = false; } - } if (nonSSLabel) { @@ -165,12 +191,10 @@ public class AlignmentAnnotation } } - } annotationId = this.hashCode() + ""; } - /** * Creates a new AlignmentAnnotation object. * @@ -186,11 +210,34 @@ public class AlignmentAnnotation int graphType) { // graphs are not editable + editable = graphType==0; + this.label = label; this.description = description; this.annotations = annotations; graph = graphType; + graphMin = min; + graphMax = max; + validateRangeAndDisplay(); + } + /** + * checks graphMin and graphMax, + * secondary structure symbols, + * sets graphType appropriately, + * sets null labels to the empty string + * if appropriate. + */ + private void validateRangeAndDisplay() { + if (annotations==null) + { + visible=false; // try to prevent renderer from displaying. + return; // this is a non-annotation row annotation - ie a sequence score. + } + + int graphType = graph; + float min = graphMin; + float max = graphMax; boolean drawValues = true; if (min == max) @@ -203,7 +250,9 @@ public class AlignmentAnnotation continue; } - if (drawValues && annotations[i].displayCharacter.length() > 1) + if (drawValues + && annotations[i].displayCharacter!=null + && annotations[i].displayCharacter.length() > 1) { drawValues = false; } @@ -238,6 +287,131 @@ public class AlignmentAnnotation } /** + * Copy constructor + * creates a new independent annotation row with the same associated sequenceRef + * @param annotation + */ + public AlignmentAnnotation(AlignmentAnnotation annotation) + { + this.label = new String(annotation.label); + if (annotation.description != null) + this.description = new String(annotation.description); + this.graphMin = annotation.graphMin; + this.graphMax = annotation.graphMax; + this.graph = annotation.graph; + this.graphHeight = annotation.graphHeight; + this.graphGroup = annotation.graphGroup; + this.editable = annotation.editable; + this.autoCalculated = annotation.autoCalculated; + this.hasIcons = annotation.hasIcons; + this.hasText = annotation.hasText; + this.height = annotation.height; + this.label = annotation.label; + this.padGaps = annotation.padGaps; + this.visible = annotation.visible; + if (this.hasScore = annotation.hasScore) + { + this.score = annotation.score; + } + if (threshold!=null) { + threshold = new GraphLine(annotation.threshold); + } + if (annotation.annotations!=null) { + Annotation[] ann = annotation.annotations; + this.annotations = new Annotation[ann.length]; + for (int i=0; i=spos && pos.intValue()<=epos) + { + newmapping.put(pos, sequenceMapping.get(pos)); + } + } + sequenceMapping.clear(); + sequenceMapping = newmapping; + } + } + annotations=temp; + } + /** + * set the annotation row to be at least length Annotations + * @param length minimum number of columns required in the annotation row + * @return false if the annotation row is greater than length + */ + public boolean padAnnotation(int length) { + if (annotations==null) + { + return true; // annotation row is correct - null == not visible and undefined length + } + if (annotations.lengthlength; + + } + + /** * DOCUMENT ME! * * @return DOCUMENT ME! @@ -310,10 +484,13 @@ public class AlignmentAnnotation { return; } - + sequenceRef=seqRef; + if (annotations==null) + { + return; + } sequenceMapping = new java.util.Hashtable(); - sequenceRef = seqRef; int seqPos; for (int i = 0; i < annotations.length; i++) @@ -337,6 +514,14 @@ public class AlignmentAnnotation public void adjustForAlignment() { + if (sequenceRef==null) + return; + + if (annotations==null) + { + return; + } + int a = 0, aSize = sequenceRef.getLength(); if (aSize == 0) @@ -362,4 +547,106 @@ public class AlignmentAnnotation annotations = temp; } + /** + * remove any null entries in annotation row and return the + * number of non-null annotation elements. + * @return + */ + private int compactAnnotationArray() { + int j=0; + for (int i=0;i