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JAL-3285 add unmerged code to SequenceGroup
author
tva
<tva@10.205.251.175>
Wed, 5 Jun 2019 13:04:52 +0000
(14:04 +0100)
committer
tva
<tva@10.205.251.175>
Wed, 5 Jun 2019 13:04:52 +0000
(14:04 +0100)
src/jalview/datamodel/SequenceGroup.java
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diff --git
a/src/jalview/datamodel/SequenceGroup.java
b/src/jalview/datamodel/SequenceGroup.java
index
56681cf
..
59cb4bb
100755
(executable)
--- a/
src/jalview/datamodel/SequenceGroup.java
+++ b/
src/jalview/datamodel/SequenceGroup.java
@@
-48,35
+48,49
@@
public class SequenceGroup implements AnnotatedCollectionI
// a subclass of ViewportProperties similarly to ViewportRanges.
// Done here as a quick fix for JAL-2665
public static final String SEQ_GROUP_CHANGED = "Sequence group changed";
// a subclass of ViewportProperties similarly to ViewportRanges.
// Done here as a quick fix for JAL-2665
public static final String SEQ_GROUP_CHANGED = "Sequence group changed";
+
+ protected PropertyChangeSupport changeSupport = new PropertyChangeSupport(
+ this);
+
+ public void addPropertyChangeListener(PropertyChangeListener listener)
+ {
+ changeSupport.addPropertyChangeListener(listener);
+ }
- private String groupName;
+ public void removePropertyChangeListener(PropertyChangeListener listener)
+ {
+ changeSupport.removePropertyChangeListener(listener);
+ }
+ // end of event notification functionality initialisation
- private String description;
+ String groupName;
- private AnnotatedCollectionI context;
+ String description;
+
+ Conservation conserve;
- private Conservation conservationData;
+ Conservation conservationData;
- private ProfilesI consensusProfiles;
+ ProfilesI consensusProfiles;
- private ProfilesI hmmProfiles;
+ ProfilesI hmmProfiles;
- private boolean displayBoxes = true;
+ boolean displayBoxes = true;
- private boolean displayText = true;
+ boolean displayText = true;
- private boolean colourText = false;
+ boolean colourText = false;
/*
* true if the group is defined as a group on the alignment, false if it is
* just a selection
*/
/*
* true if the group is defined as a group on the alignment, false if it is
* just a selection
*/
- private boolean isDefined;
+ boolean isDefined = false;
/*
* after Olivier's non-conserved only character display
*/
/*
* after Olivier's non-conserved only character display
*/
- private boolean showNonconserved;
+ boolean showNonconserved = false;
/*
* sequences in the group
/*
* sequences in the group
@@
-86,9
+100,9
@@
public class SequenceGroup implements AnnotatedCollectionI
/*
* representative sequence for this group (if any)
*/
/*
* representative sequence for this group (if any)
*/
- private SequenceI seqrep;
+ private SequenceI seqrep = null;
- private int width = -1;
+ int width = -1;
/*
* colour scheme applied to group if any
/*
* colour scheme applied to group if any
@@
-107,9
+121,9
@@
public class SequenceGroup implements AnnotatedCollectionI
public Color outlineColour = Color.black;
public Color outlineColour = Color.black;
- public Color idColour;
+ public Color idColour = null;
- public int thresholdTextColour;
+ public int thresholdTextColour = 0;
public Color textColour = Color.black;
public Color textColour = Color.black;
@@
-120,12
+134,10
@@
public class SequenceGroup implements AnnotatedCollectionI
*/
private boolean ignoreGapsInConsensus = true;
*/
private boolean ignoreGapsInConsensus = true;
- private boolean showSequenceLogo;
+ private boolean showSequenceLogo = false;
private boolean normaliseSequenceLogo;
private boolean normaliseSequenceLogo;
- private boolean showConsensusHistogram;
-
/*
* properties for HMM information annotation
*/
/*
* properties for HMM information annotation
*/
@@
-142,18
+154,23
@@
public class SequenceGroup implements AnnotatedCollectionI
/*
* visibility of rows or represented rows covered by group
*/
/*
* visibility of rows or represented rows covered by group
*/
- private boolean hidereps;
+ private boolean hidereps = false;
/*
* visibility of columns intersecting this group
*/
private boolean hidecols;
/*
* visibility of columns intersecting this group
*/
private boolean hidecols;
- private AlignmentAnnotation consensus;
+ AlignmentAnnotation consensus = null;
- private AlignmentAnnotation conservation;
+ AlignmentAnnotation conservation = null;
private AlignmentAnnotation hmmInformation;
private AlignmentAnnotation hmmInformation;
+
+ private boolean showConsensusHistogram;
+
+ private AnnotatedCollectionI context;
+
/**
* Constructor, assigning a generated default name of "JGroup:" with object
/**
* Constructor, assigning a generated default name of "JGroup:" with object
@@
-200,30
+217,17
@@
public class SequenceGroup implements AnnotatedCollectionI
* copy constructor
*
* @param seqsel
* copy constructor
*
* @param seqsel
- */
- public SequenceGroup(SequenceGroup seqsel)
- {
- this(seqsel, true);
- }
-
- /**
- * copy constructor
- *
- * @param seqsel
* @param keepsequences
* if false do not add sequences from seqsel to new instance
*/
* @param keepsequences
* if false do not add sequences from seqsel to new instance
*/
- public SequenceGroup(SequenceGroup seqsel, boolean keepsequences)
+ public SequenceGroup(SequenceGroup seqsel)
{
this();
if (seqsel != null)
{
sequences = new ArrayList<>();
{
this();
if (seqsel != null)
{
sequences = new ArrayList<>();
- if (keepsequences)
- {
- sequences.addAll(seqsel.sequences);
- }
+ sequences.addAll(seqsel.sequences);
if (seqsel.groupName != null)
{
groupName = new String(seqsel.groupName);
if (seqsel.groupName != null)
{
groupName = new String(seqsel.groupName);
@@
-258,7
+262,7
@@
public class SequenceGroup implements AnnotatedCollectionI
ignoreGapsInConsensus = seqsel.ignoreGapsInConsensus;
hmmIgnoreBelowBackground = seqsel.hmmIgnoreBelowBackground;
hmmUseInfoLetterHeight = seqsel.hmmUseInfoLetterHeight;
ignoreGapsInConsensus = seqsel.ignoreGapsInConsensus;
hmmIgnoreBelowBackground = seqsel.hmmIgnoreBelowBackground;
hmmUseInfoLetterHeight = seqsel.hmmUseInfoLetterHeight;
- if (keepsequences && seqsel.conservationData != null)
+ if (seqsel.conserve != null)
{
// todo avoid doing this if we don't actually want derived calculations
// !
{
// todo avoid doing this if we don't actually want derived calculations
// !
@@
-268,19
+272,6
@@
public class SequenceGroup implements AnnotatedCollectionI
}
}
}
}
- protected PropertyChangeSupport changeSupport = new PropertyChangeSupport(
- this);
-
- public void addPropertyChangeListener(PropertyChangeListener listener)
- {
- changeSupport.addPropertyChangeListener(listener);
- }
-
- public void removePropertyChangeListener(PropertyChangeListener listener)
- {
- changeSupport.removePropertyChangeListener(listener);
- }
-
/**
* Constructor that copies the given list of sequences
*
/**
* Constructor that copies the given list of sequences
*
@@
-297,8
+288,7
@@
public class SequenceGroup implements AnnotatedCollectionI
return showSequenceLogo;
}
return showSequenceLogo;
}
- public SequenceI[] getSelectionAsNewSequences(AlignmentI align,
- boolean copyAnnotation)
+ public SequenceI[] getSelectionAsNewSequences(AlignmentI align)
{
int iSize = sequences.size();
SequenceI[] seqs = new SequenceI[iSize];
{
int iSize = sequences.size();
SequenceI[] seqs = new SequenceI[iSize];
@@
-312,8
+302,14
@@
public class SequenceGroup implements AnnotatedCollectionI
if (seqs[ipos] != null)
{
seqs[ipos].setDescription(seq.getDescription());
if (seqs[ipos] != 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 && copyAnnotation)
+ if (seq.getAnnotation() != null)
{
AlignmentAnnotation[] alann = align.getAlignmentAnnotation();
// Only copy annotation that is either a score or referenced by the
{
AlignmentAnnotation[] alann = align.getAlignmentAnnotation();
// Only copy annotation that is either a score or referenced by the
@@
-537,7
+533,7
@@
public class SequenceGroup implements AnnotatedCollectionI
*/
public Conservation getConservation()
{
*/
public Conservation getConservation()
{
- return conservationData;
+ return conserve;
}
/**
}
/**
@@
-548,7
+544,7
@@
public class SequenceGroup implements AnnotatedCollectionI
*/
public void setConservation(Conservation c)
{
*/
public void setConservation(Conservation c)
{
- conservationData = c;
+ conserve = c;
}
/**
}
/**
@@
-609,7
+605,7
@@
public class SequenceGroup implements AnnotatedCollectionI
*/
public boolean recalcConservation()
{
*/
public boolean recalcConservation()
{
- return recalcAnnotations(false);
+ return recalcConservation(false);
}
/**
}
/**
@@
-621,7
+617,7
@@
public class SequenceGroup implements AnnotatedCollectionI
* when set, colourschemes for this group are not refreshed after
* recalculation
*/
* when set, colourschemes for this group are not refreshed after
* recalculation
*/
- public boolean recalcAnnotations(boolean defer)
+ public boolean recalcConservation(boolean defer)
{
if (cs == null && consensus == null && conservation == null
&& hmmInformation == null)
{
if (cs == null && consensus == null && conservation == null
&& hmmInformation == null)
@@
-717,6
+713,8
@@
public class SequenceGroup implements AnnotatedCollectionI
c.completeAnnotations(conservation, null, startRes, endRes + 1);
}
c.completeAnnotations(conservation, null, startRes, endRes + 1);
}
+ public ProfilesI consensusData = null;
+
private void _updateConsensusRow(ProfilesI cnsns, long nseq)
{
if (consensus == null)
private void _updateConsensusRow(ProfilesI cnsns, long nseq)
{
if (consensus == null)
@@
-725,7
+723,7
@@
public class SequenceGroup implements AnnotatedCollectionI
}
consensus.label = "Consensus for " + getName();
consensus.description = "Percent Identity";
}
consensus.label = "Consensus for " + getName();
consensus.description = "Percent Identity";
- consensusProfiles = cnsns;
+ consensusData = cnsns;
// preserve width if already set
int aWidth = (consensus.annotations != null)
? (endRes < consensus.annotations.length
// preserve width if already set
int aWidth = (consensus.annotations != null)
? (endRes < consensus.annotations.length
@@
-1323,7
+1321,7
@@
public class SequenceGroup implements AnnotatedCollectionI
ignoreGapsInConsensus = state;
}
ignoreGapsInConsensus = state;
}
- public boolean isIgnoreGapsConsensus()
+ public boolean getIgnoreGapsConsensus()
{
return ignoreGapsInConsensus;
}
{
return ignoreGapsInConsensus;
}