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JAL-1807 explicit imports (jalview.datamodel)
author
gmungoc
<g.m.carstairs@dundee.ac.uk>
Fri, 10 Jul 2015 05:14:08 +0000
(06:14 +0100)
committer
gmungoc
<g.m.carstairs@dundee.ac.uk>
Fri, 10 Jul 2015 05:14:08 +0000
(06:14 +0100)
src/jalview/datamodel/AlignedCodonFrame.java
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src/jalview/datamodel/Alignment.java
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src/jalview/datamodel/AlignmentAnnotation.java
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src/jalview/datamodel/AlignmentView.java
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src/jalview/datamodel/Mapping.java
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src/jalview/datamodel/SeqCigar.java
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src/jalview/datamodel/Sequence.java
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src/jalview/datamodel/SequenceGroup.java
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src/jalview/datamodel/xdb/embl/EmblEntry.java
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src/jalview/datamodel/xdb/embl/EmblFeatureLocations.java
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src/jalview/datamodel/xdb/embl/EmblFile.java
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diff --git
a/src/jalview/datamodel/AlignedCodonFrame.java
b/src/jalview/datamodel/AlignedCodonFrame.java
index
eb977bc
..
e48e03a
100644
(file)
--- a/
src/jalview/datamodel/AlignedCodonFrame.java
+++ b/
src/jalview/datamodel/AlignedCodonFrame.java
@@
-20,12
+20,12
@@
*/
package jalview.datamodel;
*/
package jalview.datamodel;
-import java.util.ArrayList;
-import java.util.List;
-
import jalview.util.MapList;
import jalview.util.MappingUtils;
import jalview.util.MapList;
import jalview.util.MappingUtils;
+import java.util.ArrayList;
+import java.util.List;
+
/**
* Stores mapping between the columns of a protein alignment and a DNA alignment
* and a list of individual codon to amino acid mappings between sequences.
/**
* Stores mapping between the columns of a protein alignment and a DNA alignment
* and a list of individual codon to amino acid mappings between sequences.
diff --git
a/src/jalview/datamodel/Alignment.java
b/src/jalview/datamodel/Alignment.java
index
81046f1
..
363ad0d
100755
(executable)
--- a/
src/jalview/datamodel/Alignment.java
+++ b/
src/jalview/datamodel/Alignment.java
@@
-20,6
+20,11
@@
*/
package jalview.datamodel;
*/
package jalview.datamodel;
+import jalview.analysis.AlignmentUtils;
+import jalview.io.FastaFile;
+import jalview.util.Comparison;
+import jalview.util.MessageManager;
+
import java.util.ArrayList;
import java.util.Enumeration;
import java.util.HashSet;
import java.util.ArrayList;
import java.util.Enumeration;
import java.util.HashSet;
@@
-30,10
+35,6
@@
import java.util.Map;
import java.util.Set;
import java.util.Vector;
import java.util.Set;
import java.util.Vector;
-import jalview.analysis.AlignmentUtils;
-import jalview.io.FastaFile;
-import jalview.util.MessageManager;
-
/**
* Data structure to hold and manipulate a multiple sequence alignment
*/
/**
* Data structure to hold and manipulate a multiple sequence alignment
*/
@@
-73,7
+74,7
@@
public class Alignment implements AlignmentI
{
int i = 0;
{
int i = 0;
- if (jalview.util.Comparison.isNucleotide(seqs))
+ if (Comparison.isNucleotide(seqs))
{
type = NUCLEOTIDE;
}
{
type = NUCLEOTIDE;
}
@@
-339,7
+340,7
@@
public class Alignment implements AlignmentI
/*
* (non-Javadoc)
*
/*
* (non-Javadoc)
*
- * @see jalview.datamodel.AlignmentI#findGroup(jalview.datamodel.SequenceI)
+ * @see AlignmentI#findGroup(jalview.datamodel.SequenceI)
*/
@Override
public SequenceGroup findGroup(SequenceI s)
*/
@Override
public SequenceGroup findGroup(SequenceI s)
@@
-363,7
+364,7
@@
public class Alignment implements AlignmentI
* (non-Javadoc)
*
* @see
* (non-Javadoc)
*
* @see
- * jalview.datamodel.AlignmentI#findAllGroups(jalview.datamodel.SequenceI)
+ * AlignmentI#findAllGroups(jalview.datamodel.SequenceI)
*/
@Override
public SequenceGroup[] findAllGroups(SequenceI s)
*/
@Override
public SequenceGroup[] findAllGroups(SequenceI s)
@@
-527,7
+528,7
@@
public class Alignment implements AlignmentI
/*
* (non-Javadoc)
*
/*
* (non-Javadoc)
*
- * @see jalview.datamodel.AlignmentI#findName(java.lang.String, boolean)
+ * @see AlignmentI#findName(java.lang.String, boolean)
*/
@Override
public SequenceI findName(String token, boolean b)
*/
@Override
public SequenceI findName(String token, boolean b)
@@
-538,7
+539,7
@@
public class Alignment implements AlignmentI
/*
* (non-Javadoc)
*
/*
* (non-Javadoc)
*
- * @see jalview.datamodel.AlignmentI#findName(SequenceI, java.lang.String,
+ * @see AlignmentI#findName(SequenceI, java.lang.String,
* boolean)
*/
@Override
* boolean)
*/
@Override
@@
-610,7
+611,7
@@
public class Alignment implements AlignmentI
/*
* (non-Javadoc)
*
/*
* (non-Javadoc)
*
- * @see jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SequenceI)
+ * @see AlignmentI#findIndex(jalview.datamodel.SequenceI)
*/
@Override
public int findIndex(SequenceI s)
*/
@Override
public int findIndex(SequenceI s)
@@
-634,7
+635,7
@@
public class Alignment implements AlignmentI
* (non-Javadoc)
*
* @see
* (non-Javadoc)
*
* @see
- * jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SearchResults)
+ * AlignmentI#findIndex(jalview.datamodel.SearchResults)
*/
@Override
public int findIndex(SearchResults results)
*/
@Override
public int findIndex(SearchResults results)
@@
-718,7
+719,7
@@
public class Alignment implements AlignmentI
/*
* (non-Javadoc)
*
/*
* (non-Javadoc)
*
- * @see jalview.datamodel.AlignmentI#isAligned()
+ * @see AlignmentI#isAligned()
*/
@Override
public boolean isAligned()
*/
@Override
public boolean isAligned()
@@
-729,7
+730,7
@@
public class Alignment implements AlignmentI
/*
* (non-Javadoc)
*
/*
* (non-Javadoc)
*
- * @see jalview.datamodel.AlignmentI#isAligned(boolean)
+ * @see AlignmentI#isAligned(boolean)
*/
@Override
public boolean isAligned(boolean includeHidden)
*/
@Override
public boolean isAligned(boolean includeHidden)
@@
-778,7
+779,7
@@
public class Alignment implements AlignmentI
/*
* (non-Javadoc)
*
/*
* (non-Javadoc)
*
- * @seejalview.datamodel.AlignmentI#deleteAnnotation(jalview.datamodel.
+ * @seeAlignmentI#deleteAnnotation(jalview.datamodel.
* AlignmentAnnotation)
*/
@Override
* AlignmentAnnotation)
*/
@Override
@@
-852,7
+853,7
@@
public class Alignment implements AlignmentI
/*
* (non-Javadoc)
*
/*
* (non-Javadoc)
*
- * @seejalview.datamodel.AlignmentI#addAnnotation(jalview.datamodel.
+ * @seeAlignmentI#addAnnotation(jalview.datamodel.
* AlignmentAnnotation)
*/
@Override
* AlignmentAnnotation)
*/
@Override
@@
-864,7
+865,7
@@
public class Alignment implements AlignmentI
/*
* (non-Javadoc)
*
/*
* (non-Javadoc)
*
- * @seejalview.datamodel.AlignmentI#addAnnotation(jalview.datamodel.
+ * @seeAlignmentI#addAnnotation(jalview.datamodel.
* AlignmentAnnotation, int)
*/
@Override
* AlignmentAnnotation, int)
*/
@Override
@@
-1072,7
+1073,7
@@
public class Alignment implements AlignmentI
for (int j = current.getLength(); j > maxLength; j--)
{
if (j > maxLength
for (int j = current.getLength(); j > maxLength; j--)
{
if (j > maxLength
- && !jalview.util.Comparison.isGap(current.getCharAt(j)))
+ && !Comparison.isGap(current.getCharAt(j)))
{
maxLength = j;
break;
{
maxLength = j;
break;
@@
-1128,7
+1129,7
@@
public class Alignment implements AlignmentI
boolean hitres = false;
for (int j = 0, rs = 0, ssiz = current.getLength(); j < ssiz; j++)
{
boolean hitres = false;
for (int j = 0, rs = 0, ssiz = current.getLength(); j < ssiz; j++)
{
- if (!jalview.util.Comparison.isGap(current.getCharAt(j)))
+ if (!Comparison.isGap(current.getCharAt(j)))
{
if (!hitres)
{
{
if (!hitres)
{
@@
-1264,7
+1265,7
@@
public class Alignment implements AlignmentI
* (non-Javadoc)
*
* @see
* (non-Javadoc)
*
* @see
- * jalview.datamodel.AlignmentI#addCodonFrame(jalview.datamodel.AlignedCodonFrame
+ * AlignmentI#addCodonFrame(jalview.datamodel.AlignedCodonFrame
* )
*/
@Override
* )
*/
@Override
@@
-1280,7
+1281,7
@@
public class Alignment implements AlignmentI
* (non-Javadoc)
*
* @see
* (non-Javadoc)
*
* @see
- * jalview.datamodel.AlignmentI#getCodonFrame(jalview.datamodel.SequenceI)
+ * AlignmentI#getCodonFrame(jalview.datamodel.SequenceI)
*/
@Override
public List<AlignedCodonFrame> getCodonFrame(SequenceI seq)
*/
@Override
public List<AlignedCodonFrame> getCodonFrame(SequenceI seq)
@@
-1303,7
+1304,7
@@
public class Alignment implements AlignmentI
/**
* Sets the codon frame mappings (replacing any existing mappings).
*
/**
* Sets the codon frame mappings (replacing any existing mappings).
*
- * @see jalview.datamodel.AlignmentI#setCodonFrames()
+ * @see AlignmentI#setCodonFrames()
*/
@Override
public void setCodonFrames(Set<AlignedCodonFrame> acfs)
*/
@Override
public void setCodonFrames(Set<AlignedCodonFrame> acfs)
@@
-1315,7
+1316,7
@@
public class Alignment implements AlignmentI
* Returns the set of codon frame mappings. Any changes to the returned set
* will affect the alignment.
*
* Returns the set of codon frame mappings. Any changes to the returned set
* will affect the alignment.
*
- * @see jalview.datamodel.AlignmentI#getCodonFrames()
+ * @see AlignmentI#getCodonFrames()
*/
@Override
public Set<AlignedCodonFrame> getCodonFrames()
*/
@Override
public Set<AlignedCodonFrame> getCodonFrames()
@@
-1326,7
+1327,7
@@
public class Alignment implements AlignmentI
/*
* (non-Javadoc)
*
/*
* (non-Javadoc)
*
- * @seejalview.datamodel.AlignmentI#removeCodonFrame(jalview.datamodel.
+ * @seeAlignmentI#removeCodonFrame(jalview.datamodel.
* AlignedCodonFrame)
*/
@Override
* AlignedCodonFrame)
*/
@Override
diff --git
a/src/jalview/datamodel/AlignmentAnnotation.java
b/src/jalview/datamodel/AlignmentAnnotation.java
index
322fd54
..
f6b633c
100755
(executable)
--- a/
src/jalview/datamodel/AlignmentAnnotation.java
+++ b/
src/jalview/datamodel/AlignmentAnnotation.java
@@
-20,6
+20,11
@@
*/
package jalview.datamodel;
*/
package jalview.datamodel;
+import jalview.analysis.Rna;
+import jalview.analysis.SecStrConsensus.SimpleBP;
+import jalview.analysis.WUSSParseException;
+import jalview.schemes.ResidueProperties;
+
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
@@
-28,10
+33,6
@@
import java.util.Iterator;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Map;
import java.util.Map.Entry;
-import jalview.analysis.Rna;
-import jalview.analysis.SecStrConsensus.SimpleBP;
-import jalview.analysis.WUSSParseException;
-
/**
* DOCUMENT ME!
*
/**
* DOCUMENT ME!
*
@@
-417,9
+418,9
@@
public class AlignmentAnnotation
&& firstChar != 'Y'
&& firstChar != 'Z'
&& firstChar != '-'
&& firstChar != 'Y'
&& firstChar != 'Z'
&& firstChar != '-'
- && firstChar < jalview.schemes.ResidueProperties.aaIndex.length)
+ && firstChar < ResidueProperties.aaIndex.length)
{
{
- if (jalview.schemes.ResidueProperties.aaIndex[firstChar] < 23) // TODO:
+ if (ResidueProperties.aaIndex[firstChar] < 23) // TODO:
// parameterise
// to
// gap
// parameterise
// to
// gap
diff --git
a/src/jalview/datamodel/AlignmentView.java
b/src/jalview/datamodel/AlignmentView.java
index
b36a0a5
..
5457fbc
100644
(file)
--- a/
src/jalview/datamodel/AlignmentView.java
+++ b/
src/jalview/datamodel/AlignmentView.java
@@
-109,7
+109,7
@@
public class AlignmentView
boolean recordGroups)
{
// refactored from AlignViewport.getAlignmentView(selectedOnly);
boolean recordGroups)
{
// refactored from AlignViewport.getAlignmentView(selectedOnly);
- this(new jalview.datamodel.CigarArray(alignment,
+ this(new CigarArray(alignment,
(hasHiddenColumns ? columnSelection : null),
(selectedRegionOnly ? selection : null)),
(selectedRegionOnly && selection != null) ? selection
(hasHiddenColumns ? columnSelection : null),
(selectedRegionOnly ? selection : null)),
(selectedRegionOnly && selection != null) ? selection
diff --git
a/src/jalview/datamodel/Mapping.java
b/src/jalview/datamodel/Mapping.java
index
d7b7eb9
..
5a31d68
100644
(file)
--- a/
src/jalview/datamodel/Mapping.java
+++ b/
src/jalview/datamodel/Mapping.java
@@
-20,12
+20,12
@@
*/
package jalview.datamodel;
*/
package jalview.datamodel;
+import jalview.util.MapList;
+
import java.util.Iterator;
import java.util.NoSuchElementException;
import java.util.Vector;
import java.util.Iterator;
import java.util.NoSuchElementException;
import java.util.Vector;
-import jalview.util.MapList;
-
public class Mapping
{
/**
public class Mapping
{
/**
diff --git
a/src/jalview/datamodel/SeqCigar.java
b/src/jalview/datamodel/SeqCigar.java
index
09b2e89
..
b6c8cdc
100644
(file)
--- a/
src/jalview/datamodel/SeqCigar.java
+++ b/
src/jalview/datamodel/SeqCigar.java
@@
-20,14
+20,15
@@
*/
package jalview.datamodel;
*/
package jalview.datamodel;
-import java.util.Enumeration;
-import java.util.Hashtable;
-
import jalview.analysis.AlignSeq;
import jalview.analysis.SeqsetUtils;
import jalview.analysis.AlignSeq;
import jalview.analysis.SeqsetUtils;
+import jalview.util.Comparison;
import jalview.util.MessageManager;
import jalview.util.ShiftList;
import jalview.util.MessageManager;
import jalview.util.ShiftList;
+import java.util.Enumeration;
+import java.util.Hashtable;
+
public class SeqCigar extends CigarSimple
{
/**
public class SeqCigar extends CigarSimple
{
/**
@@
-165,7
+166,7
@@
public class SeqCigar extends CigarSimple
{
// make a new dataset sequence
String ungapped = AlignSeq.extractGaps(
{
// make a new dataset sequence
String ungapped = AlignSeq.extractGaps(
- jalview.util.Comparison.GapChars, new String(seq_string));
+ Comparison.GapChars, new String(seq_string));
l_ungapped = ungapped.length();
// check that we haven't just duplicated an ungapped sequence.
if (l_ungapped == seq.getLength())
l_ungapped = ungapped.length();
// check that we haven't just duplicated an ungapped sequence.
if (l_ungapped == seq.getLength())
@@
-318,7
+319,7
@@
public class SeqCigar extends CigarSimple
while (p <= endpos)
{
while (p <= endpos)
{
- boolean isGap = (p < res) ? jalview.util.Comparison.isGap(seq
+ boolean isGap = (p < res) ? Comparison.isGap(seq
.getCharAt(p)) : true;
if ((startpos <= p) && (p <= endpos))
{
.getCharAt(p)) : true;
if ((startpos <= p) && (p <= endpos))
{
diff --git
a/src/jalview/datamodel/Sequence.java
b/src/jalview/datamodel/Sequence.java
index
c78ec22
..
e1f9d00
100755
(executable)
--- a/
src/jalview/datamodel/Sequence.java
+++ b/
src/jalview/datamodel/Sequence.java
@@
-21,6
+21,8
@@
package jalview.datamodel;
import jalview.analysis.AlignSeq;
package jalview.datamodel;
import jalview.analysis.AlignSeq;
+import jalview.schemes.ResidueProperties;
+import jalview.util.Comparison;
import jalview.util.StringUtils;
import java.util.ArrayList;
import jalview.util.StringUtils;
import java.util.ArrayList;
@@
-28,6
+30,8
@@
import java.util.Enumeration;
import java.util.List;
import java.util.Vector;
import java.util.List;
import java.util.Vector;
+import com.stevesoft.pat.Regex;
+
import fr.orsay.lri.varna.models.rna.RNA;
/**
import fr.orsay.lri.varna.models.rna.RNA;
/**
@@
-119,10
+123,9
@@
public class Sequence extends ASequence implements SequenceI
checkValidRange();
}
checkValidRange();
}
- com.stevesoft.pat.Regex limitrx = new com.stevesoft.pat.Regex(
- "[/][0-9]{1,}[-][0-9]{1,}$");
+ Regex limitrx = new Regex("[/][0-9]{1,}[-][0-9]{1,}$");
- com.stevesoft.pat.Regex endrx = new com.stevesoft.pat.Regex("[0-9]{1,}$");
+ Regex endrx = new Regex("[0-9]{1,}$");
void parseId()
{
void parseId()
{
@@
-151,7
+154,7
@@
public class Sequence extends ASequence implements SequenceI
int endRes = 0;
for (int j = 0; j < sequence.length; j++)
{
int endRes = 0;
for (int j = 0; j < sequence.length; j++)
{
- if (!jalview.util.Comparison.isGap(sequence[j]))
+ if (!Comparison.isGap(sequence[j]))
{
endRes++;
}
{
endRes++;
}
@@
-643,7
+646,7
@@
public class Sequence extends ASequence implements SequenceI
// Rely on end being at least as long as the length of the sequence.
while ((i < sequence.length) && (j <= end) && (j <= pos))
{
// Rely on end being at least as long as the length of the sequence.
while ((i < sequence.length) && (j <= end) && (j <= pos))
{
- if (!jalview.util.Comparison.isGap(sequence[i]))
+ if (!Comparison.isGap(sequence[i]))
{
j++;
}
{
j++;
}
@@
-669,7
+672,7
@@
public class Sequence extends ASequence implements SequenceI
int seqlen = sequence.length;
while ((j < i) && (j < seqlen))
{
int seqlen = sequence.length;
while ((j < i) && (j < seqlen))
{
- if (!jalview.util.Comparison.isGap(sequence[j]))
+ if (!Comparison.isGap(sequence[j]))
{
pos++;
}
{
pos++;
}
@@
-689,15
+692,15
@@
public class Sequence extends ASequence implements SequenceI
*/
public int[] gapMap()
{
*/
public int[] gapMap()
{
- String seq = jalview.analysis.AlignSeq.extractGaps(
- jalview.util.Comparison.GapChars, new String(sequence));
+ String seq = AlignSeq.extractGaps(
+ Comparison.GapChars, new String(sequence));
int[] map = new int[seq.length()];
int j = 0;
int p = 0;
while (j < sequence.length)
{
int[] map = new int[seq.length()];
int j = 0;
int p = 0;
while (j < sequence.length)
{
- if (!jalview.util.Comparison.isGap(sequence[j]))
+ if (!Comparison.isGap(sequence[j]))
{
map[p++] = j;
}
{
map[p++] = j;
}
@@
-718,7
+721,7
@@
public class Sequence extends ASequence implements SequenceI
while ((j < seqlen))
{
map[j] = pos;
while ((j < seqlen))
{
map[j] = pos;
- if (!jalview.util.Comparison.isGap(sequence[j]))
+ if (!Comparison.isGap(sequence[j]))
{
pos++;
}
{
pos++;
}
@@
-737,7
+740,7
@@
public class Sequence extends ASequence implements SequenceI
int seqlen = sequence.length;
while ((j < seqlen))
{
int seqlen = sequence.length;
while ((j < seqlen))
{
- if (jalview.util.Comparison.isGap(sequence[j]))
+ if (Comparison.isGap(sequence[j]))
{
if (lastj == -1)
{
{
if (lastj == -1)
{
@@
-781,7
+784,7
@@
public class Sequence extends ASequence implements SequenceI
boolean ecalc = false, scalc = false;
for (int s = i; s < j; s++)
{
boolean ecalc = false, scalc = false;
for (int s = i; s < j; s++)
{
- if (jalview.schemes.ResidueProperties.aaIndex[sequence[s]] != 23)
+ if (ResidueProperties.aaIndex[sequence[s]] != 23)
{
if (createNewDs)
{
{
if (createNewDs)
{
@@
-1001,7
+1004,7
@@
public class Sequence extends ASequence implements SequenceI
}
for (int i = 0; i < sequence.length; i++)
{
}
for (int i = 0; i < sequence.length; i++)
{
- if (jalview.util.Comparison.isGap(sequence[i]))
+ if (Comparison.isGap(sequence[i]))
{
return false;
}
{
return false;
}
@@
-1030,7
+1033,7
@@
public class Sequence extends ASequence implements SequenceI
// Create a new, valid dataset sequence
SequenceI ds = seq;
ds.setSequence(AlignSeq.extractGaps(
// Create a new, valid dataset sequence
SequenceI ds = seq;
ds.setSequence(AlignSeq.extractGaps(
- jalview.util.Comparison.GapChars, new String(sequence)));
+ Comparison.GapChars, new String(sequence)));
setDatasetSequence(ds);
ds.setSequenceFeatures(getSequenceFeatures());
seq = this; // and return this sequence as the derived sequence.
setDatasetSequence(ds);
ds.setSequenceFeatures(getSequenceFeatures());
seq = this; // and return this sequence as the derived sequence.
@@
-1049,7
+1052,7
@@
public class Sequence extends ASequence implements SequenceI
if (datasetSequence == null)
{
datasetSequence = new Sequence(getName(), AlignSeq.extractGaps(
if (datasetSequence == null)
{
datasetSequence = new Sequence(getName(), AlignSeq.extractGaps(
- jalview.util.Comparison.GapChars, getSequenceAsString()),
+ Comparison.GapChars, getSequenceAsString()),
getStart(), getEnd());
datasetSequence.setSequenceFeatures(getSequenceFeatures());
datasetSequence.setDescription(getDescription());
getStart(), getEnd());
datasetSequence.setSequenceFeatures(getSequenceFeatures());
datasetSequence.setDescription(getDescription());
diff --git
a/src/jalview/datamodel/SequenceGroup.java
b/src/jalview/datamodel/SequenceGroup.java
index
3439248
..
2fe03e1
100755
(executable)
--- a/
src/jalview/datamodel/SequenceGroup.java
+++ b/
src/jalview/datamodel/SequenceGroup.java
@@
-20,6
+20,12
@@
*/
package jalview.datamodel;
*/
package jalview.datamodel;
+import jalview.analysis.AAFrequency;
+import jalview.analysis.Conservation;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ResidueProperties;
+import jalview.util.Comparison;
+
import java.awt.Color;
import java.util.ArrayList;
import java.util.Hashtable;
import java.awt.Color;
import java.util.ArrayList;
import java.util.Hashtable;
@@
-27,11
+33,6
@@
import java.util.List;
import java.util.Map;
import java.util.Vector;
import java.util.Map;
import java.util.Vector;
-import jalview.analysis.AAFrequency;
-import jalview.analysis.Conservation;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ResidueProperties;
-
/**
* Collects a set contiguous ranges on a set of sequences
*
/**
* Collects a set contiguous ranges on a set of sequences
*
@@
-280,7
+281,7
@@
public class SequenceGroup implements AnnotatedCollectionI
for (int j = 0; j < endRes + 1 && j < seq.getLength(); j++)
{
ch = seq.getCharAt(j);
for (int j = 0; j < endRes + 1 && j < seq.getLength(); j++)
{
ch = seq.getCharAt(j);
- if (!jalview.util.Comparison.isGap((ch)))
+ if (!Comparison.isGap((ch)))
{
eres++;
}
{
eres++;
}
diff --git
a/src/jalview/datamodel/xdb/embl/EmblEntry.java
b/src/jalview/datamodel/xdb/embl/EmblEntry.java
index
9c9447e
..
4241990
100644
(file)
--- a/
src/jalview/datamodel/xdb/embl/EmblEntry.java
+++ b/
src/jalview/datamodel/xdb/embl/EmblEntry.java
@@
-27,6
+27,8
@@
import jalview.datamodel.Mapping;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.util.DBRefUtils;
+import jalview.util.MapList;
import java.util.Hashtable;
import java.util.Map.Entry;
import java.util.Hashtable;
import java.util.Map.Entry;
@@
-392,7
+394,7
@@
public class EmblEntry
* don't return any translated protein sequences marked in features
* @return dataset sequences with DBRefs and features - DNA always comes first
*/
* don't return any translated protein sequences marked in features
* @return dataset sequences with DBRefs and features - DNA always comes first
*/
- public jalview.datamodel.SequenceI[] getSequences(boolean noNa,
+ public SequenceI[] getSequences(boolean noNa,
boolean noPeptide, String sourceDb)
{ // TODO: ensure emblEntry.getSequences behaves correctly for returning all
// cases of noNa and noPeptide
boolean noPeptide, String sourceDb)
{ // TODO: ensure emblEntry.getSequences behaves correctly for returning all
// cases of noNa and noPeptide
@@
-496,7
+498,7
@@
public class EmblEntry
{
boolean isEmblCdna = sourceDb.equals(DBRefSource.EMBLCDS);
// extract coding region(s)
{
boolean isEmblCdna = sourceDb.equals(DBRefSource.EMBLCDS);
// extract coding region(s)
- jalview.datamodel.Mapping map = null;
+ Mapping map = null;
int[] exon = null;
if (feature.locations != null)
{
int[] exon = null;
if (feature.locations != null)
{
@@
-601,7
+603,7
@@
public class EmblEntry
// marked.
exon = new int[]
{ dna.getStart() + (prstart - 1), dna.getEnd() };
// marked.
exon = new int[]
{ dna.getStart() + (prstart - 1), dna.getEnd() };
- map = new jalview.datamodel.Mapping(product, exon, new int[]
+ map = new Mapping(product, exon, new int[]
{ 1, prseq.length() }, 3, 1);
}
if ((prseq.length() + 1) * 3 == (1 - prstart + dna.getSequence().length))
{ 1, prseq.length() }, 3, 1);
}
if ((prseq.length() + 1) * 3 == (1 - prstart + dna.getSequence().length))
@@
-610,7
+612,7
@@
public class EmblEntry
.println("Allowing for additional stop codon at end of cDNA fragment... will probably cause an error in VAMSAs!");
exon = new int[]
{ dna.getStart() + (prstart - 1), dna.getEnd() - 3 };
.println("Allowing for additional stop codon at end of cDNA fragment... will probably cause an error in VAMSAs!");
exon = new int[]
{ dna.getStart() + (prstart - 1), dna.getEnd() - 3 };
- map = new jalview.datamodel.Mapping(product, exon, new int[]
+ map = new Mapping(product, exon, new int[]
{ 1, prseq.length() }, 3, 1);
}
}
{ 1, prseq.length() }, 3, 1);
}
}
@@
-631,7
+633,7
@@
public class EmblEntry
{
// final product length trunctation check
{
// final product length trunctation check
- map = new jalview.datamodel.Mapping(product,
+ map = new Mapping(product,
adjustForProteinLength(prseq.length(), exon), new int[]
{ 1, prseq.length() }, 3, 1);
// reconstruct the EMBLCDS entry
adjustForProteinLength(prseq.length(), exon), new int[]
{ 1, prseq.length() }, 3, 1);
// reconstruct the EMBLCDS entry
@@
-641,7
+643,7
@@
public class EmblEntry
pcdnaref.setAccessionId(prid);
pcdnaref.setSource(DBRefSource.EMBLCDS);
pcdnaref.setVersion(getVersion()); // same as parent EMBL version.
pcdnaref.setAccessionId(prid);
pcdnaref.setSource(DBRefSource.EMBLCDS);
pcdnaref.setVersion(getVersion()); // same as parent EMBL version.
- jalview.util.MapList mp = new jalview.util.MapList(new int[]
+ MapList mp = new MapList(new int[]
{ 1, prseq.length() }, new int[]
{ 1 + (prstart - 1), (prstart - 1) + 3 * prseq.length() }, 1, 3);
// { 1 + (prstart - 1) * 3,
{ 1, prseq.length() }, new int[]
{ 1 + (prstart - 1), (prstart - 1) + 3 * prseq.length() }, 1, 3);
// { 1 + (prstart - 1) * 3,
@@
-686,10
+688,10
@@
public class EmblEntry
{
for (DBRefEntry ref : feature.dbRefs)
{
{
for (DBRefEntry ref : feature.dbRefs)
{
- ref.setSource(jalview.util.DBRefUtils.getCanonicalName(ref
+ ref.setSource(DBRefUtils.getCanonicalName(ref
.getSource()));
// Hard code the kind of protein product accessions that EMBL cite
.getSource()));
// Hard code the kind of protein product accessions that EMBL cite
- if (ref.getSource().equals(jalview.datamodel.DBRefSource.UNIPROT))
+ if (ref.getSource().equals(DBRefSource.UNIPROT))
{
ref.setMap(map);
if (map != null && map.getTo() != null)
{
ref.setMap(map);
if (map != null && map.getTo() != null)
@@
-700,7
+702,7
@@
public class EmblEntry
if (map.getTo().getName().indexOf(prid) == 0)
{
map.getTo().setName(
if (map.getTo().getName().indexOf(prid) == 0)
{
map.getTo().setName(
- jalview.datamodel.DBRefSource.UNIPROT + "|"
+ DBRefSource.UNIPROT + "|"
+ ref.getAccessionId());
}
}
+ ref.getAccessionId());
}
}
diff --git
a/src/jalview/datamodel/xdb/embl/EmblFeatureLocations.java
b/src/jalview/datamodel/xdb/embl/EmblFeatureLocations.java
index
eb0bee7
..
4f9e5fa
100644
(file)
--- a/
src/jalview/datamodel/xdb/embl/EmblFeatureLocations.java
+++ b/
src/jalview/datamodel/xdb/embl/EmblFeatureLocations.java
@@
-20,6
+20,8
@@
*/
package jalview.datamodel.xdb.embl;
*/
package jalview.datamodel.xdb.embl;
+import jalview.bin.Cache;
+
import java.util.Vector;
/**
import java.util.Vector;
/**
@@
-150,9
+152,9
@@
public class EmblFeatureLocations
}
else if (locationType != null)
{
}
else if (locationType != null)
{
- if (jalview.bin.Cache.log != null)
+ if (Cache.log != null)
{
{
- jalview.bin.Cache.log
+ Cache.log
.error("EmbleFeatureLocations.getElementRanges cannot deal with locationType=='"
+ locationType + "'");
}
.error("EmbleFeatureLocations.getElementRanges cannot deal with locationType=='"
+ locationType + "'");
}
diff --git
a/src/jalview/datamodel/xdb/embl/EmblFile.java
b/src/jalview/datamodel/xdb/embl/EmblFile.java
index
2129054
..
f3475d7
100644
(file)
--- a/
src/jalview/datamodel/xdb/embl/EmblFile.java
+++ b/
src/jalview/datamodel/xdb/embl/EmblFile.java
@@
-20,6
+20,8
@@
*/
package jalview.datamodel.xdb.embl;
*/
package jalview.datamodel.xdb.embl;
+import jalview.bin.Cache;
+
import java.io.File;
import java.io.FileReader;
import java.io.PrintWriter;
import java.io.File;
import java.io.FileReader;
import java.io.PrintWriter;
@@
-116,11
+118,11
@@
public class EmblFile
try
{
// uncomment to DEBUG EMBLFile reading
try
{
// uncomment to DEBUG EMBLFile reading
- if (jalview.bin.Cache.getDefault(
- jalview.bin.Cache.CASTORLOGLEVEL, "debug")
+ if (Cache.getDefault(
+ Cache.CASTORLOGLEVEL, "debug")
.equalsIgnoreCase("DEBUG"))
{
.equalsIgnoreCase("DEBUG"))
{
- unmar.setDebug(jalview.bin.Cache.log.isDebugEnabled());
+ unmar.setDebug(Cache.log.isDebugEnabled());
}
} catch (Exception e)
{
}
} catch (Exception e)
{