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JAL-2388 Comment typo
[jalview.git]
/
src
/
jalview
/
analysis
/
AAFrequency.java
diff --git
a/src/jalview/analysis/AAFrequency.java
b/src/jalview/analysis/AAFrequency.java
index
569b036
..
17874e6
100755
(executable)
--- a/
src/jalview/analysis/AAFrequency.java
+++ b/
src/jalview/analysis/AAFrequency.java
@@
-20,11
+20,16
@@
*/
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.Profiles;
+import jalview.datamodel.ProfilesI;
+import jalview.datamodel.ResidueCount;
+import jalview.datamodel.ResidueCount.SymbolCounts;
import jalview.datamodel.SequenceI;
import jalview.ext.android.SparseIntArray;
import jalview.util.Comparison;
import jalview.datamodel.SequenceI;
import jalview.ext.android.SparseIntArray;
import jalview.util.Comparison;
@@
-47,18
+52,8
@@
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
+67,13
@@
public class AAFrequency
}
}
}
}
- public static final Profile[] calculate(List<SequenceI> list,
+ public static final ProfilesI 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 ProfilesI 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()];
@@
-88,20
+83,19
@@
public class AAFrequency
for (int i = 0; i < sequences.size(); i++)
{
seqs[i] = sequences.get(i);
for (int i = 0; i < sequences.size(); i++)
{
seqs[i] = sequences.get(i);
- if (seqs[i].getLength() > width)
+ int length = seqs[i].getLength();
+ if (length > width)
{
{
- width = seqs[i].getLength();
+ width = length;
}
}
}
}
- Profile[] reply = new Profile[width];
-
if (end >= width)
{
end = width;
}
if (end >= width)
{
end = width;
}
- calculate(seqs, start, end, reply, profile);
+ ProfilesI reply = calculate(seqs, width, start, end, profile);
return reply;
}
}
return reply;
}
}
@@
-110,17
+104,17
@@
public class AAFrequency
* Calculate the consensus symbol(s) for each column in the given range.
*
* @param sequences
* Calculate the consensus symbol(s) for each column in the given range.
*
* @param sequences
+ * @param width
+ * the full width of the alignment
* @param start
* start column (inclusive, base zero)
* @param end
* end column (exclusive)
* @param start
* start column (inclusive, base zero)
* @param end
* end column (exclusive)
- * @param result
- * array in which to store profile per column
* @param saveFullProfile
* if true, store all symbol counts
*/
* @param saveFullProfile
* if true, store all symbol counts
*/
- public static final void calculate(final SequenceI[] sequences,
- int start, int end, Profile[] result, boolean saveFullProfile)
+ public static final ProfilesI calculate(final SequenceI[] sequences,
+ int width, int start, int end, boolean saveFullProfile)
{
// long now = System.currentTimeMillis();
int seqCount = sequences.length;
{
// long now = System.currentTimeMillis();
int seqCount = sequences.length;
@@
-128,6
+122,8
@@
public class AAFrequency
int nucleotideCount = 0;
int peptideCount = 0;
int nucleotideCount = 0;
int peptideCount = 0;
+ ProfileI[] result = new ProfileI[width];
+
for (int column = start; column < end; column++)
{
/*
for (int column = start; column < end; column++)
{
/*
@@
-180,7
+176,7
@@
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)
@@
-190,6
+186,7
@@
public class AAFrequency
result[column] = profile;
}
result[column] = profile;
}
+ return new Profiles(result);
// long elapsed = System.currentTimeMillis() - now;
// System.out.println(elapsed);
}
// long elapsed = System.currentTimeMillis() - now;
// System.out.println(elapsed);
}
@@
-228,10
+225,10
@@
public class AAFrequency
* the annotation row to add annotations to
* @param profiles
* the source consensus data
* the annotation row to add annotations to
* @param profiles
* the source consensus data
- * @param iStart
- * start column
- * @param width
- * end column
+ * @param startCol
+ * start column (inclusive)
+ * @param endCol
+ * end column (exclusive)
* @param ignoreGaps
* if true, normalise residue percentages ignoring gaps
* @param showSequenceLogo
* @param ignoreGaps
* if true, normalise residue percentages ignoring gaps
* @param showSequenceLogo
@@
-241,12
+238,12
@@
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,
+ ProfilesI profiles, int startCol, int endCol, boolean ignoreGaps,
boolean showSequenceLogo, long nseq)
{
// long now = System.currentTimeMillis();
if (consensus == null || consensus.annotations == null
boolean showSequenceLogo, long nseq)
{
// long now = System.currentTimeMillis();
if (consensus == null || consensus.annotations == null
- || consensus.annotations.length < width)
+ || consensus.annotations.length < endCol)
{
/*
* called with a bad alignment annotation row
{
/*
* called with a bad alignment annotation row
@@
-255,28
+252,37
@@
public class AAFrequency
return;
}
return;
}
- final int dp = getPercentageDp(nseq);
-
- for (int i = iStart; i < width; i++)
+ for (int i = startCol; i < endCol; i++)
{
{
- Profile profile;
- if (i >= profiles.length || ((profile = profiles[i]) == null))
+ ProfileI profile = profiles.get(i);
+ if (profile == null)
{
/*
* happens if sequences calculated over were
* shorter than alignment width
*/
consensus.annotations[i] = null;
{
/*
* happens if sequences calculated over were
* shorter than alignment width
*/
consensus.annotations[i] = null;
- continue;
+ return;
}
}
+ final int dp = getPercentageDp(nseq);
+
float value = profile.getPercentageIdentity(ignoreGaps);
String description = getTooltip(profile, value, showSequenceLogo,
ignoreGaps, dp);
float value = profile.getPercentageIdentity(ignoreGaps);
String description = getTooltip(profile, value, showSequenceLogo,
ignoreGaps, dp);
- consensus.annotations[i] = new Annotation(profile.getModalResidue(),
- description, ' ', value);
+ 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;
// System.out.println(-elapsed);
}
// long elapsed = System.currentTimeMillis() - now;
// System.out.println(-elapsed);
@@
-300,7
+306,7
@@
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();
@@
-318,15
+324,18
@@
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;
@@
-348,7
+357,7
@@
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];