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JAL-4386 PCA/Tree Calculation for Secondary Structures: Changes related to dropdown...
[jalview.git]
/
src
/
jalview
/
analysis
/
AlignmentUtils.java
diff --git
a/src/jalview/analysis/AlignmentUtils.java
b/src/jalview/analysis/AlignmentUtils.java
index
1158c53
..
be5133f
100644
(file)
--- a/
src/jalview/analysis/AlignmentUtils.java
+++ b/
src/jalview/analysis/AlignmentUtils.java
@@
-547,7
+547,8
@@
public class AlignmentUtils
if (translated == null || !(aaRes == translated.charAt(0)))
{
// debug
if (translated == null || !(aaRes == translated.charAt(0)))
{
// debug
- // System.out.println(("Mismatch at " + i + "/" + aaResidue + ": "
+ // jalview.bin.Console.outPrintln(("Mismatch at " + i + "/" + aaResidue
+ // + ": "
// + codon + "(" + translated + ") != " + aaRes));
return false;
}
// + codon + "(" + translated + ") != " + aaRes));
return false;
}
@@
-698,7
+699,8
@@
public class AlignmentUtils
* unmapped position; treat like a gap
*/
sourceGapMappedLength += ratio;
* unmapped position; treat like a gap
*/
sourceGapMappedLength += ratio;
- // System.err.println("Can't align: no codon mapping to residue "
+ // jalview.bin.Console.errPrintln("Can't align: no codon mapping to
+ // residue "
// + sourceDsPos + "(" + sourceChar + ")");
// return;
continue;
// + sourceDsPos + "(" + sourceChar + ")");
// return;
continue;
@@
-883,7
+885,8
@@
public class AlignmentUtils
{
if (protein.isNucleotide() || !dna.isNucleotide())
{
{
if (protein.isNucleotide() || !dna.isNucleotide())
{
- System.err.println("Wrong alignment type in alignProteinAsDna");
+ jalview.bin.Console
+ .errPrintln("Wrong alignment type in alignProteinAsDna");
return 0;
}
List<SequenceI> unmappedProtein = new ArrayList<>();
return 0;
}
List<SequenceI> unmappedProtein = new ArrayList<>();
@@
-908,7
+911,8
@@
public class AlignmentUtils
{
if (protein.isNucleotide() || !dna.isNucleotide())
{
{
if (protein.isNucleotide() || !dna.isNucleotide())
{
- System.err.println("Wrong alignment type in alignProteinAsDna");
+ jalview.bin.Console
+ .errPrintln("Wrong alignment type in alignProteinAsDna");
return 0;
}
// todo: implement this
return 0;
}
// todo: implement this
@@
-988,7
+992,7
@@
public class AlignmentUtils
.getLength() == mappedFromLength - 1);
if (cdsLength != mappedToLength && !addStopCodon)
{
.getLength() == mappedFromLength - 1);
if (cdsLength != mappedToLength && !addStopCodon)
{
- System.err.println(String.format(
+ jalview.bin.Console.errPrintln(String.format(
"Can't align cds as protein (length mismatch %d/%d): %s",
cdsLength, mappedToLength, cdsSeq.getName()));
}
"Can't align cds as protein (length mismatch %d/%d): %s",
cdsLength, mappedToLength, cdsSeq.getName()));
}
@@
-1162,7
+1166,7
@@
public class AlignmentUtils
AlignedCodon codon = sequenceCodon.getValue();
if (codon.peptideCol > 1)
{
AlignedCodon codon = sequenceCodon.getValue();
if (codon.peptideCol > 1)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Problem mapping protein with >1 unmapped start positions: "
+ seq.getName());
}
"Problem mapping protein with >1 unmapped start positions: "
+ seq.getName());
}
@@
-1512,7
+1516,9
@@
public class AlignmentUtils
* @param alignment
* the alignment to add them to
* @param selectionGroup
* @param alignment
* the alignment to add them to
* @param selectionGroup
- * current selection group (or null if none)
+ * current selection group - may be null, if provided then any added
+ * annotation will be trimmed to just those columns in the selection
+ * group
*/
public static void addReferenceAnnotations(
Map<SequenceI, List<AlignmentAnnotation>> annotations,
*/
public static void addReferenceAnnotations(
Map<SequenceI, List<AlignmentAnnotation>> annotations,
@@
-1536,7
+1542,9
@@
public class AlignmentUtils
* @param seq
* @param ann
* @param selectionGroup
* @param seq
* @param ann
* @param selectionGroup
- * - may be null
+ * current selection group - may be null, if provided then any added
+ * annotation will be trimmed to just those columns in the selection
+ * group
* @return annotation added to {@code seq and {@code alignment}
*/
public static AlignmentAnnotation addReferenceAnnotationTo(
* @return annotation added to {@code seq and {@code alignment}
*/
public static AlignmentAnnotation addReferenceAnnotationTo(
@@
-2770,8
+2778,8
@@
public class AlignmentUtils
fromRange[i + 1]);
if (range == null)
{
fromRange[i + 1]);
if (range == null)
{
- System.err.println("Error in mapping " + seqMap + " from "
- + fromSeq.getName());
+ jalview.bin.Console.errPrintln("Error in mapping " + seqMap
+ + " from " + fromSeq.getName());
return false;
}
int fromCol = fromSeq.findIndex(fromRange[i]);
return false;
}
int fromCol = fromSeq.findIndex(fromRange[i]);