X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=326793d054437d76271172dfd8a7646603cd1cb7;hb=b117912a656de4b937e3684d58254c215b357ad5;hp=20b23a9a0365fd60766b2d1ae099bf52d6099032;hpb=7f964795c092e1bf4fbee18904b3d3dc1c29ddf8;p=jalview.git diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java index 20b23a9..326793d 100755 --- a/src/jalview/datamodel/SequenceGroup.java +++ b/src/jalview/datamodel/SequenceGroup.java @@ -20,19 +20,21 @@ */ package jalview.datamodel; -import jalview.analysis.AAFrequency; -import jalview.analysis.Conservation; -import jalview.renderer.ResidueShader; -import jalview.renderer.ResidueShaderI; -import jalview.schemes.ColourSchemeI; - import java.awt.Color; import java.beans.PropertyChangeListener; import java.beans.PropertyChangeSupport; import java.util.ArrayList; +import java.util.Arrays; +import java.util.Collection; import java.util.List; import java.util.Map; +import jalview.analysis.AAFrequency; +import jalview.analysis.Conservation; +import jalview.renderer.ResidueShader; +import jalview.renderer.ResidueShaderI; +import jalview.schemes.ColourSchemeI; + /** * Collects a set contiguous ranges on a set of sequences * @@ -87,7 +89,7 @@ public class SequenceGroup implements AnnotatedCollectionI /** * group members */ - private List sequences = new ArrayList<>(); + private List sequences; /** * representative sequence for this group (if any) @@ -101,11 +103,15 @@ public class SequenceGroup implements AnnotatedCollectionI */ public ResidueShaderI cs; - // start column (base 0) - int startRes = 0; + /** + * start column (base 0) + */ + private int startRes = 0; - // end column (base 0) - int endRes = 0; + /** + * end column (base 0) + */ + private int endRes = 0; public Color outlineColour = Color.black; @@ -157,6 +163,7 @@ public class SequenceGroup implements AnnotatedCollectionI { groupName = "JGroup:" + this.hashCode(); cs = new ResidueShader(); + sequences = new ArrayList<>(); } /** @@ -184,19 +191,7 @@ public class SequenceGroup implements AnnotatedCollectionI this.displayText = displayText; this.colourText = colourText; this.cs = new ResidueShader(scheme); - - if (start > 0) // sanity check for negative start column positions - { - startRes = start; - } - else - { - jalview.bin.Cache.log.warn( - "Negative start column index detected, resetting to default index: " - + startRes); - // start = startRes; - } - + startRes = start; endRes = end; recalcConservation(); } @@ -220,20 +215,8 @@ public class SequenceGroup implements AnnotatedCollectionI displayBoxes = seqsel.displayBoxes; displayText = seqsel.displayText; colourText = seqsel.colourText; - - if (seqsel.startRes > 0) // sanity check for negative start column - // positions - { - startRes = seqsel.startRes; - } - else - { - jalview.bin.Cache.log.warn( - "Negative start column index detected, resetting to default index: " - + startRes); - // seqsel.startRes = startRes; - } - + + startRes = seqsel.startRes; endRes = seqsel.endRes; cs = new ResidueShader((ResidueShader) seqsel.cs); if (seqsel.description != null) @@ -262,6 +245,17 @@ public class SequenceGroup implements AnnotatedCollectionI } } + /** + * Constructor that copies the given list of sequences + * + * @param seqs + */ + public SequenceGroup(List seqs) + { + this(); + this.sequences.addAll(seqs); + } + public boolean isShowSequenceLogo() { return showSequenceLogo; @@ -276,18 +270,10 @@ public class SequenceGroup implements AnnotatedCollectionI for (int i = 0, ipos = 0; i < inorder.length; i++) { SequenceI seq = inorder[i]; - - seqs[ipos] = seq.getSubSequence(startRes, endRes + 1); - if (seqs[ipos] != null) + SequenceI seqipos = seqs[ipos] = seq.getSubSequence(startRes, + endRes + 1); + if (seqipos != null) { - seqs[ipos].setDescription(seq.getDescription()); - seqs[ipos].setDBRefs(seq.getDBRefs()); - seqs[ipos].setSequenceFeatures(seq.getSequenceFeatures()); - if (seq.getDatasetSequence() != null) - { - seqs[ipos].setDatasetSequence(seq.getDatasetSequence()); - } - if (seq.getAnnotation() != null) { AlignmentAnnotation[] alann = align.getAlignmentAnnotation(); @@ -299,7 +285,7 @@ public class SequenceGroup implements AnnotatedCollectionI if (alann != null) { boolean found = false; - for (int pos = 0; pos < alann.length; pos++) + for (int pos = 0, np = alann.length; pos < np; pos++) { if (alann[pos] == tocopy) { @@ -317,7 +303,12 @@ public class SequenceGroup implements AnnotatedCollectionI newannot.restrict(startRes, endRes); newannot.setSequenceRef(seqs[ipos]); newannot.adjustForAlignment(); - seqs[ipos].addAlignmentAnnotation(newannot); + ContactMatrixI cm = seq.getContactMatrixFor(seq.getAnnotation()[a]); + if (cm!=null) + { + seqs[ipos].addContactListFor(newannot, cm); + } + seqipos.addAlignmentAnnotation(newannot); } } ipos++; @@ -776,13 +767,15 @@ public class SequenceGroup implements AnnotatedCollectionI /** * Set the first column selected by this group. Runs from 0<=i 1 && desc.charAt(0) == '[') { - seqs.append(consensus.annotations[i].description.charAt(1)); + seqs.append(desc.charAt(1)); } else { @@ -1341,39 +1335,16 @@ public class SequenceGroup implements AnnotatedCollectionI @Override public Iterable findAnnotation(String calcId) { - List aa = new ArrayList<>(); - if (calcId == null) - { - return aa; - } - for (AlignmentAnnotation a : getAlignmentAnnotation()) - { - if (calcId.equals(a.getCalcId())) - { - aa.add(a); - } - } - return aa; + return AlignmentAnnotation.findAnnotation( + Arrays.asList(getAlignmentAnnotation()), calcId); } @Override public Iterable findAnnotations(SequenceI seq, String calcId, String label) { - ArrayList aa = new ArrayList<>(); - for (AlignmentAnnotation ann : getAlignmentAnnotation()) - { - if ((calcId == null || (ann.getCalcId() != null - && ann.getCalcId().equals(calcId))) - && (seq == null || (ann.sequenceRef != null - && ann.sequenceRef == seq)) - && (label == null - || (ann.label != null && ann.label.equals(label)))) - { - aa.add(ann); - } - } - return aa; + return AlignmentAnnotation.findAnnotations( + Arrays.asList(getAlignmentAnnotation()), seq, calcId, label); } /** @@ -1384,17 +1355,8 @@ public class SequenceGroup implements AnnotatedCollectionI */ public boolean hasAnnotation(String calcId) { - if (calcId != null && !"".equals(calcId)) - { - for (AlignmentAnnotation a : getAlignmentAnnotation()) - { - if (a.getCalcId() == calcId) - { - return true; - } - } - } - return false; + return AlignmentAnnotation + .hasAnnotation(Arrays.asList(getAlignmentAnnotation()), calcId); } /** @@ -1521,4 +1483,51 @@ public class SequenceGroup implements AnnotatedCollectionI { return (startRes <= apos && endRes >= apos) && sequences.contains(seq); } + + //// + //// Contact Matrix Holder Boilerplate + //// + ContactMapHolder cmholder = new ContactMapHolder(); + + @Override + public Collection getContactMaps() + { + return cmholder.getContactMaps(); + } + + @Override + public ContactMatrixI getContactMatrixFor(AlignmentAnnotation ann) + { + return cmholder.getContactMatrixFor(ann); + } + + @Override + public ContactListI getContactListFor(AlignmentAnnotation _aa, int column) + { + return cmholder.getContactListFor(_aa, column); + } + + @Override + public AlignmentAnnotation addContactList(ContactMatrixI cm) + { + AlignmentAnnotation aa = cmholder.addContactList(cm); + + Annotation _aa[] = new Annotation[getWidth()]; + Annotation dummy = new Annotation(0.0f); + for (int i = 0; i < _aa.length; _aa[i++] = dummy) + { + ; + } + aa.annotations = _aa; + // TODO passing annotations back to context to be added + return aa; + } + + @Override + public void addContactListFor(AlignmentAnnotation annotation, + ContactMatrixI cm) + { + cmholder.addContactListFor(annotation, cm); + } + }