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sequence is char []
author
amwaterhouse
<Andrew Waterhouse>
Tue, 5 Dec 2006 17:56:07 +0000
(17:56 +0000)
committer
amwaterhouse
<Andrew Waterhouse>
Tue, 5 Dec 2006 17:56:07 +0000
(17:56 +0000)
14 files changed:
src/MCview/PDBChain.java
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src/jalview/analysis/AAFrequency.java
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src/jalview/analysis/AlignSeq.java
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src/jalview/analysis/AlignmentSorter.java
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src/jalview/analysis/Conservation.java
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src/jalview/analysis/NJTree.java
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src/jalview/analysis/SeqsetUtils.java
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src/jalview/appletgui/AlignViewport.java
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src/jalview/appletgui/FeatureRenderer.java
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src/jalview/appletgui/Finder.java
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src/jalview/appletgui/RedundancyPanel.java
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src/jalview/appletgui/SequenceRenderer.java
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src/jalview/appletgui/UserDefinedColours.java
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src/jalview/util/Comparison.java
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diff --git
a/src/MCview/PDBChain.java
b/src/MCview/PDBChain.java
index
ddf05e1
..
0cb9f02
100755
(executable)
--- a/
src/MCview/PDBChain.java
+++ b/
src/MCview/PDBChain.java
@@
-236,15
+236,15
@@
public class PDBChain {
try {
\r
b = (Bond) bonds.elementAt(i);
\r
\r
try {
\r
b = (Bond) bonds.elementAt(i);
\r
\r
- ( (Bond) bonds.elementAt(i)).startCol = cs.findColour(
\r
- ResidueProperties.aa[ ( (Integer) ResidueProperties.aa3Hash.
\r
- get(b.at1.resName)).intValue()]
\r
+ /* ( (Bond) bonds.elementAt(i)).startCol = cs.findColour(
\r
+ ResidueProperties.codonTranslate(
\r
+ ResidueProperties.aa3Hash.get(b.at1.resName).toString().charAt(0)
\r
);
\r
\r
b.endCol = cs.findColour(
\r
ResidueProperties.aa[ ( (Integer) ResidueProperties.aa3Hash.
\r
get(b.at2.resName)).intValue()]
\r
);
\r
\r
b.endCol = cs.findColour(
\r
ResidueProperties.aa[ ( (Integer) ResidueProperties.aa3Hash.
\r
get(b.at2.resName)).intValue()]
\r
- );
\r
+ );*/
\r
\r
} catch (Exception e)
\r
{
\r
\r
} catch (Exception e)
\r
{
\r
diff --git
a/src/jalview/analysis/AAFrequency.java
b/src/jalview/analysis/AAFrequency.java
index
e2dd6f1
..
3d91080
100755
(executable)
--- a/
src/jalview/analysis/AAFrequency.java
+++ b/
src/jalview/analysis/AAFrequency.java
@@
-75,7
+75,7
@@
public static final void calculate(SequenceI[] sequences,
\r
int[] values = new int[132];
\r
\r
\r
int[] values = new int[132];
\r
\r
- String seq;
\r
+ char [] seq;
\r
\r
for (i = start; i < end; i++)
\r
{
\r
\r
for (i = start; i < end; i++)
\r
{
\r
@@
-88,9
+88,9
@@
public static final void calculate(SequenceI[] sequences,
for (j = 0; j < jSize; j++)
\r
{
\r
seq = sequences[j].getSequence();
\r
for (j = 0; j < jSize; j++)
\r
{
\r
seq = sequences[j].getSequence();
\r
- if (seq.length() > i)
\r
+ if (seq.length > i)
\r
{
\r
{
\r
- c = seq.charAt(i);
\r
+ c = seq[i];
\r
\r
if(c == '.' || c==' ')
\r
c = '-';
\r
\r
if(c == '.' || c==' ')
\r
c = '-';
\r
diff --git
a/src/jalview/analysis/AlignSeq.java
b/src/jalview/analysis/AlignSeq.java
index
0af85f1
..
d0c5869
100755
(executable)
--- a/
src/jalview/analysis/AlignSeq.java
+++ b/
src/jalview/analysis/AlignSeq.java
@@
-106,7
+106,7
@@
public class AlignSeq
*/
\r
public AlignSeq(SequenceI s1, SequenceI s2, String type)
\r
{
\r
*/
\r
public AlignSeq(SequenceI s1, SequenceI s2, String type)
\r
{
\r
- SeqInit(s1, s1.getSequence(), s2, s2.getSequence(), type);
\r
+ SeqInit(s1, s1.getSequenceAsString(), s2, s2.getSequenceAsString(), type);
\r
}
\r
\r
/**
\r
}
\r
\r
/**
\r
diff --git
a/src/jalview/analysis/AlignmentSorter.java
b/src/jalview/analysis/AlignmentSorter.java
index
bf18b70
..
24f2ddf
100755
(executable)
--- a/
src/jalview/analysis/AlignmentSorter.java
+++ b/
src/jalview/analysis/AlignmentSorter.java
@@
-52,8
+52,8
@@
public class AlignmentSorter
\r
for (int i = 0; i < nSeq; i++)
\r
{
\r
\r
for (int i = 0; i < nSeq; i++)
\r
{
\r
- scores[i] = Comparison.PID(align.getSequenceAt(i).getSequence(),
\r
- s.getSequence());
\r
+ scores[i] = Comparison.PID(align.getSequenceAt(i).getSequenceAsString(),
\r
+ s.getSequenceAsString());
\r
seqs[i] = align.getSequenceAt(i);
\r
}
\r
\r
seqs[i] = align.getSequenceAt(i);
\r
}
\r
\r
diff --git
a/src/jalview/analysis/Conservation.java
b/src/jalview/analysis/Conservation.java
index
1342e93
..
6098465
100755
(executable)
--- a/
src/jalview/analysis/Conservation.java
+++ b/
src/jalview/analysis/Conservation.java
@@
-100,7
+100,7
@@
public class Conservation
if ((i > -1) && (i < sSize))
{
if ((i > -1) && (i < sSize))
{
- sq = sequences[i].getSequence();
+ sq = sequences[i].getSequenceAsString();
if (seqNums.size() <= i)
{
if (seqNums.size() <= i)
{
diff --git
a/src/jalview/analysis/NJTree.java
b/src/jalview/analysis/NJTree.java
index
78c4e60
..
6f89754
100755
(executable)
--- a/
src/jalview/analysis/NJTree.java
+++ b/
src/jalview/analysis/NJTree.java
@@
-298,7
+298,7
@@
public class NJTree
leaf.setElement(new Sequence(leaf.getName(), "THISISAPLACEHLDER"));
}
leaf.setPlaceholder(true);
leaf.setElement(new Sequence(leaf.getName(), "THISISAPLACEHLDER"));
}
leaf.setPlaceholder(true);
-
+
}
}
}
}
}
}
@@
-680,8
+680,8
@@
public class NJTree
try
{
score += ResidueProperties.getBLOSUM62(
try
{
score += ResidueProperties.getBLOSUM62(
- sequenceString[i].substring(k, k + 1),
- sequenceString[j].substring(k, k + 1));
+ sequenceString[i].charAt(k),
+ sequenceString[j].charAt(k));
}
catch (Exception ex)
{
}
catch (Exception ex)
{
diff --git
a/src/jalview/analysis/SeqsetUtils.java
b/src/jalview/analysis/SeqsetUtils.java
index
885305a
..
00fbad5
100755
(executable)
--- a/
src/jalview/analysis/SeqsetUtils.java
+++ b/
src/jalview/analysis/SeqsetUtils.java
@@
-204,7
+204,10
@@
public class SeqsetUtils
boolean ungapped[] = new boolean[sequences.length];
int msflen=0;
for (int i=0,j=sequences.length; i<j;i++) {
boolean ungapped[] = new boolean[sequences.length];
int msflen=0;
for (int i=0,j=sequences.length; i<j;i++) {
- String tempseq = jalview.analysis.AlignSeq.extractGaps(jalview.util.Comparison.GapChars, sequences[i].getSequence());
+ String tempseq = jalview.analysis.AlignSeq.extractGaps(
+ jalview.util.Comparison.GapChars,
+ sequences[i].getSequenceAsString());
+
if (tempseq.length()==0)
ungapped[i]=false;
else {
if (tempseq.length()==0)
ungapped[i]=false;
else {
diff --git
a/src/jalview/appletgui/AlignViewport.java
b/src/jalview/appletgui/AlignViewport.java
index
40d67b0
..
ad7113a
100755
(executable)
--- a/
src/jalview/appletgui/AlignViewport.java
+++ b/
src/jalview/appletgui/AlignViewport.java
@@
-296,7
+296,7
@@
public class AlignViewport
cons.findQuality();
\r
}
\r
\r
cons.findQuality();
\r
}
\r
\r
- String sequence = cons.getConsSequence().getSequence();
\r
+ char [] sequence = cons.getConsSequence().getSequence();
\r
float minR;
\r
float minG;
\r
float minB;
\r
float minR;
\r
float minG;
\r
float minB;
\r
@@
-331,7
+331,7
@@
public class AlignViewport
{
\r
float value = 0;
\r
\r
{
\r
float value = 0;
\r
\r
- c = sequence.charAt(i);
\r
+ c = sequence[i];
\r
\r
if (Character.isDigit(c))
\r
value = (int) (c - '0');
\r
\r
if (Character.isDigit(c))
\r
value = (int) (c - '0');
\r
@@
-1201,7
+1201,7
@@
public class AlignViewport
}
\r
else
\r
{
\r
}
\r
else
\r
{
\r
- selection[i] = seqs[i].getSequence(start, end);
\r
+ selection[i] = seqs[i].getSequenceAsString(start, end);
\r
}
\r
}
\r
\r
}
\r
}
\r
\r
diff --git
a/src/jalview/appletgui/FeatureRenderer.java
b/src/jalview/appletgui/FeatureRenderer.java
index
a24525e
..
47fbb0d
100755
(executable)
--- a/
src/jalview/appletgui/FeatureRenderer.java
+++ b/
src/jalview/appletgui/FeatureRenderer.java
@@
-293,7
+293,7
@@
public class FeatureRenderer
\r
for (i = fstart; i <= fend; i++)
\r
{
\r
\r
for (i = fstart; i <= fend; i++)
\r
{
\r
- s = seq.getSequence().charAt(i);
\r
+ s = seq.getCharAt(i);
\r
\r
if (jalview.util.Comparison.isGap(s))
\r
{
\r
\r
if (jalview.util.Comparison.isGap(s))
\r
{
\r
@@
-412,10
+412,10
@@
public class FeatureRenderer
{
\r
void setTransparency(Graphics g, float value)
\r
{
\r
{
\r
void setTransparency(Graphics g, float value)
\r
{
\r
- Graphics2D g2 = (Graphics2D) g;
\r
+ /* Graphics2D g2 = (Graphics2D) g;
\r
g2.setComposite(
\r
AlphaComposite.getInstance(
\r
g2.setComposite(
\r
AlphaComposite.getInstance(
\r
- AlphaComposite.SRC_OVER, value));
\r
+ AlphaComposite.SRC_OVER, value));*/
\r
}
\r
}
\r
\r
}
\r
}
\r
\r
diff --git
a/src/jalview/appletgui/Finder.java
b/src/jalview/appletgui/Finder.java
index
52be802
..
4c195e8
100755
(executable)
--- a/
src/jalview/appletgui/Finder.java
+++ b/
src/jalview/appletgui/Finder.java
@@
-191,7
+191,7
@@
public class Finder extends Panel implements ActionListener
continue;
\r
}
\r
\r
continue;
\r
}
\r
\r
- item = seq.getSequence();
\r
+ item = seq.getSequenceAsString();
\r
if(!caseSensitive.getState())
\r
item = item.toUpperCase();
\r
\r
if(!caseSensitive.getState())
\r
item = item.toUpperCase();
\r
\r
diff --git
a/src/jalview/appletgui/RedundancyPanel.java
b/src/jalview/appletgui/RedundancyPanel.java
index
fccc30f
..
fd85ce7
100755
(executable)
--- a/
src/jalview/appletgui/RedundancyPanel.java
+++ b/
src/jalview/appletgui/RedundancyPanel.java
@@
-143,8
+143,8
@@
public class RedundancyPanel extends SliderPanel implements Runnable, WindowList
\r
if(omitHidden==null)
\r
{
\r
\r
if(omitHidden==null)
\r
{
\r
- seqi = originalSequences[i].getSequence(start, end);
\r
- seqj = originalSequences[j].getSequence(start, end);
\r
+ seqi = originalSequences[i].getSequenceAsString(start, end);
\r
+ seqj = originalSequences[j].getSequenceAsString(start, end);
\r
}
\r
else
\r
{
\r
}
\r
else
\r
{
\r
diff --git
a/src/jalview/appletgui/SequenceRenderer.java
b/src/jalview/appletgui/SequenceRenderer.java
index
480a506
..
04defb7
100755
(executable)
--- a/
src/jalview/appletgui/SequenceRenderer.java
+++ b/
src/jalview/appletgui/SequenceRenderer.java
@@
-76,7
+76,7
@@
public class SequenceRenderer
{
\r
if (cs != null)
\r
{
\r
{
\r
if (cs != null)
\r
{
\r
- resBoxColour = cs.findColour(seq.getSequence(i, i + 1), i);
\r
+ resBoxColour = cs.findColour(seq.getCharAt(i), i);
\r
}
\r
else if(forOverview && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
\r
{
\r
}
\r
else if(forOverview && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
\r
{
\r
@@
-293,7
+293,7
@@
public class SequenceRenderer
{
\r
if (i < seq.getLength())
\r
{
\r
{
\r
if (i < seq.getLength())
\r
{
\r
- s = seq.getSequence().charAt(i);
\r
+ s = seq.getCharAt(i);
\r
}
\r
\r
charOffset = (av.charWidth - fm.charWidth(s)) / 2;
\r
}
\r
\r
charOffset = (av.charWidth - fm.charWidth(s)) / 2;
\r
diff --git
a/src/jalview/appletgui/UserDefinedColours.java
b/src/jalview/appletgui/UserDefinedColours.java
index
20f68b4
..
b9c0950
100755
(executable)
--- a/
src/jalview/appletgui/UserDefinedColours.java
+++ b/
src/jalview/appletgui/UserDefinedColours.java
@@
-248,7
+248,7
@@
public class UserDefinedColours
\r
try
\r
{
\r
\r
try
\r
{
\r
- col = oldColourScheme.findColour(aa, -1);
\r
+ col = oldColourScheme.findColour(aa.charAt(0), -1);
\r
}
\r
catch (Exception ex)
\r
{}
\r
}
\r
catch (Exception ex)
\r
{}
\r
diff --git
a/src/jalview/util/Comparison.java
b/src/jalview/util/Comparison.java
index
6c7197a
..
50472a5
100755
(executable)
--- a/
src/jalview/util/Comparison.java
+++ b/
src/jalview/util/Comparison.java
@@
-55,8
+55,8
@@
public class Comparison
*/
\r
public static float compare(SequenceI ii, SequenceI jj, int start, int end)
\r
{
\r
*/
\r
public static float compare(SequenceI ii, SequenceI jj, int start, int end)
\r
{
\r
- String si = ii.getSequence();
\r
- String sj = jj.getSequence();
\r
+ String si = ii.getSequenceAsString();
\r
+ String sj = jj.getSequenceAsString();
\r
\r
int ilen = si.length() - 1;
\r
int jlen = sj.length() - 1;
\r
\r
int ilen = si.length() - 1;
\r
int jlen = sj.length() - 1;
\r