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JAL-2320 added getViewer() method to return Chimera or Jmol panel
[jalview.git]
/
src
/
jalview
/
analysis
/
AAFrequency.java
diff --git
a/src/jalview/analysis/AAFrequency.java
b/src/jalview/analysis/AAFrequency.java
index
5ecd644
..
6bdffe1
100755
(executable)
--- a/
src/jalview/analysis/AAFrequency.java
+++ b/
src/jalview/analysis/AAFrequency.java
@@
-20,12
+20,15
@@
*/
package jalview.analysis;
*/
package jalview.analysis;
-import jalview.analysis.ResidueCount.SymbolCounts;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
+import jalview.datamodel.Profile;
+import jalview.datamodel.ProfileI;
+import jalview.datamodel.ResidueCount;
import jalview.datamodel.SequenceI;
import jalview.datamodel.SequenceI;
+import jalview.datamodel.ResidueCount.SymbolCounts;
import jalview.ext.android.SparseIntArray;
import jalview.util.Comparison;
import jalview.util.Format;
import jalview.ext.android.SparseIntArray;
import jalview.util.Comparison;
import jalview.util.Format;
@@
-47,18
+50,8
@@
import java.util.List;
*/
public class AAFrequency
{
*/
public class AAFrequency
{
- public static final String MAXCOUNT = "C";
-
- public static final String MAXRESIDUE = "R";
-
- public static final String PID_GAPS = "G";
-
- public static final String PID_NOGAPS = "N";
-
public static final String PROFILE = "P";
public static final String PROFILE = "P";
- public static final String ENCODED_CHARS = "E";
-
/*
* Quick look-up of String value of char 'A' to 'Z'
*/
/*
* Quick look-up of String value of char 'A' to 'Z'
*/
@@
-72,13
+65,13
@@
public class AAFrequency
}
}
}
}
- public static final Profile[] calculate(List<SequenceI> list,
+ public static final ProfileI[] calculate(List<SequenceI> list,
int start, int end)
{
return calculate(list, start, end, false);
}
int start, int end)
{
return calculate(list, start, end, false);
}
- public static final Profile[] calculate(List<SequenceI> sequences,
+ public static final ProfileI[] calculate(List<SequenceI> sequences,
int start, int end, boolean profile)
{
SequenceI[] seqs = new SequenceI[sequences.size()];
int start, int end, boolean profile)
{
SequenceI[] seqs = new SequenceI[sequences.size()];
@@
-94,7
+87,7
@@
public class AAFrequency
}
}
}
}
- Profile[] reply = new Profile[width];
+ ProfileI[] reply = new ProfileI[width];
if (end >= width)
{
if (end >= width)
{
@@
-111,14
+104,16
@@
public class AAFrequency
*
* @param sequences
* @param start
*
* @param sequences
* @param start
+ * start column (inclusive, base zero)
* @param end
* @param end
+ * end column (exclusive)
* @param result
* array in which to store profile per column
* @param saveFullProfile
* if true, store all symbol counts
*/
public static final void calculate(final SequenceI[] sequences,
* @param result
* array in which to store profile per column
* @param saveFullProfile
* if true, store all symbol counts
*/
public static final void calculate(final SequenceI[] sequences,
- int start, int end, Profile[] result, boolean saveFullProfile)
+ int start, int end, ProfileI[] result, boolean saveFullProfile)
{
// long now = System.currentTimeMillis();
int seqCount = sequences.length;
{
// long now = System.currentTimeMillis();
int seqCount = sequences.length;
@@
-169,8
+164,7
@@
public class AAFrequency
else
{
/*
else
{
/*
- * here we count a gap if the sequence doesn't
- * reach this column (is that correct?)
+ * count a gap if the sequence doesn't reach this column
*/
residueCounts.addGap();
}
*/
residueCounts.addGap();
}
@@
-179,7
+173,7
@@
public class AAFrequency
int maxCount = residueCounts.getModalCount();
String maxResidue = residueCounts.getResiduesForCount(maxCount);
int gapCount = residueCounts.getGapCount();
int maxCount = residueCounts.getModalCount();
String maxResidue = residueCounts.getResiduesForCount(maxCount);
int gapCount = residueCounts.getGapCount();
- Profile profile = new Profile(seqCount, gapCount, maxCount,
+ ProfileI profile = new Profile(seqCount, gapCount, maxCount,
maxResidue);
if (saveFullProfile)
maxResidue);
if (saveFullProfile)
@@
-220,8
+214,8
@@
public class AAFrequency
/**
* Derive the consensus annotations to be added to the alignment for display.
* This does not recompute the raw data, but may be called on a change in
/**
* Derive the consensus annotations to be added to the alignment for display.
* This does not recompute the raw data, but may be called on a change in
- * display options, such as 'show logo', which may in turn result in a change
- * in the derived values.
+ * display options, such as 'ignore gaps', which may in turn result in a
+ * change in the derived values.
*
* @param consensus
* the annotation row to add annotations to
*
* @param consensus
* the annotation row to add annotations to
@@
-240,7
+234,7
@@
public class AAFrequency
* number of sequences
*/
public static void completeConsensus(AlignmentAnnotation consensus,
* number of sequences
*/
public static void completeConsensus(AlignmentAnnotation consensus,
- Profile[] profiles, int iStart, int width, boolean ignoreGaps,
+ ProfileI[] profiles, int iStart, int width, boolean ignoreGaps,
boolean showSequenceLogo, long nseq)
{
// long now = System.currentTimeMillis();
boolean showSequenceLogo, long nseq)
{
// long now = System.currentTimeMillis();
@@
-258,7
+252,7
@@
public class AAFrequency
for (int i = iStart; i < width; i++)
{
for (int i = iStart; i < width; i++)
{
- Profile profile;
+ ProfileI profile;
if (i >= profiles.length || ((profile = profiles[i]) == null))
{
/*
if (i >= profiles.length || ((profile = profiles[i]) == null))
{
/*
@@
-274,7
+268,16
@@
public class AAFrequency
String description = getTooltip(profile, value, showSequenceLogo,
ignoreGaps, dp);
String description = getTooltip(profile, value, showSequenceLogo,
ignoreGaps, dp);
- consensus.annotations[i] = new Annotation(profile.getModalResidue(),
+ String modalResidue = profile.getModalResidue();
+ if ("".equals(modalResidue))
+ {
+ modalResidue = "-";
+ }
+ else if (modalResidue.length() > 1)
+ {
+ modalResidue = "+";
+ }
+ consensus.annotations[i] = new Annotation(modalResidue,
description, ' ', value);
}
// long elapsed = System.currentTimeMillis() - now;
description, ' ', value);
}
// long elapsed = System.currentTimeMillis() - now;
@@
-299,7
+302,7
@@
public class AAFrequency
* the number of decimal places to format percentages to
* @return
*/
* the number of decimal places to format percentages to
* @return
*/
- static String getTooltip(Profile profile, float pid,
+ static String getTooltip(ProfileI profile, float pid,
boolean showSequenceLogo, boolean ignoreGaps, int dp)
{
ResidueCount counts = profile.getCounts();
boolean showSequenceLogo, boolean ignoreGaps, int dp)
{
ResidueCount counts = profile.getCounts();
@@
-317,15
+320,18
@@
public class AAFrequency
String maxRes = profile.getModalResidue();
if (maxRes.length() > 1)
{
String maxRes = profile.getModalResidue();
if (maxRes.length() > 1)
{
- sb.append("[").append(maxRes).append("] ");
- maxRes = "+";
+ sb.append("[").append(maxRes).append("]");
}
else
{
}
else
{
- sb.append(maxRes).append(" ");
+ sb.append(maxRes);
+ }
+ if (maxRes.length() > 0)
+ {
+ sb.append(" ");
+ Format.appendPercentage(sb, pid, dp);
+ sb.append("%");
}
}
- Format.appendPercentage(sb, pid, dp);
- sb.append("%");
description = sb.toString();
}
return description;
description = sb.toString();
}
return description;
@@
-347,7
+353,7
@@
public class AAFrequency
* calculations
* @return
*/
* calculations
* @return
*/
- public static int[] extractProfile(Profile profile,
+ public static int[] extractProfile(ProfileI profile,
boolean ignoreGaps)
{
int[] rtnval = new int[64];
boolean ignoreGaps)
{
int[] rtnval = new int[64];