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andrewyatzandrewyatz
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Modified in line with latest version of biojava3-core's Sequence interface
git-svn-id: http://code.open-bio.org/repos/biojava/biojava-live/trunk@8391 7c6358e6-4a41-0410-a743-a5b2a554c398
1 parent b19532a commit ee47db7

3 files changed

Lines changed: 19 additions & 24 deletions

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‎biojava3-alignment/src/main/java/org/biojava3/alignment/SimpleAlignedSequence.java‎

Lines changed: 8 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -37,6 +37,7 @@
3737
import org.biojava3.core.sequence.template.Compound;
3838
import org.biojava3.core.sequence.template.CompoundSet;
3939
import org.biojava3.core.sequence.template.Sequence;
40+
import org.biojava3.core.sequence.template.SequenceMixin;
4041
import org.biojava3.core.sequence.template.SequenceView;
4142

4243
/**
@@ -303,22 +304,12 @@ public int getLength() {
303304

304305
@Override
305306
public String getSequenceAsString() {
306-
return getSequenceAsString(1, length, Strand.UNDEFINED);
307-
}
308-
309-
@Override
310-
public String getSequenceAsString(Integer start, Integer end, Strand strand) {
311-
StringBuilder s = new StringBuilder();
312-
for (C compound : getAsList().subList(start - 1, end)) {
313-
s.append(compound == null ? gap : getCompoundSet().getStringForCompound(compound));
314-
}
315-
return s.toString();
307+
return SequenceMixin.toString(this);
316308
}
317309

318310
@Override
319311
public SequenceView<C> getSubSequence(Integer start, Integer end) {
320-
// TODO SequenceView<C> getSubSequence(Integer start, Integer end)
321-
return null;
312+
return SequenceMixin.createSubSequence(this, start, end);
322313
}
323314

324315
// method for Iterable
@@ -379,4 +370,9 @@ private void setLocation(List<Step> steps) {
379370
}
380371
}
381372

373+
@Override
374+
//TODO Needs to implements
375+
public SequenceView<C> getReverse() {
376+
throw new UnsupportedOperationException("Not supported yet.");
377+
}
382378
}

‎biojava3-alignment/src/main/java/org/biojava3/alignment/SimpleProfile.java‎

Lines changed: 8 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -480,7 +480,7 @@ private String toString(int width, String header, String idFormat, boolean seqIn
480480
s.append(String.format(seqIndexFormatPre, as.getSequenceIndexAt(start)));
481481
}
482482

483-
s.append(as.getSequenceAsString(start, end, Strand.UNDEFINED));
483+
s.append(as.getSubSequence(start, end).getSequenceAsString());
484484

485485
if (seqIndexPost) {
486486
s.append(String.format(seqIndexFormatPost, as.getSequenceIndexAt(end)));
@@ -505,7 +505,7 @@ private String toString(int width, String header, String idFormat, boolean seqIn
505505
if (seqIndexPre) {
506506
s.append(String.format(seqIndexFormatPre, as.getSequenceIndexAt(start)));
507507
}
508-
s.append(as.getSequenceAsString(start, end, Strand.UNDEFINED));
508+
s.append(as.getSubSequence(start, end).getSequenceAsString());
509509
if (seqIndexPost) {
510510
s.append(String.format(seqIndexFormatPost, as.getSequenceIndexAt(end)));
511511
}
@@ -546,11 +546,10 @@ private void printSequenceAlignmentWeb(StringBuilder s,
546546
s.append(String.format(seqIndexFormatPre, as.getSequenceIndexAt(start)));
547547
}
548548

549-
550-
String mySeq = as.getSequenceAsString(start, end, Strand.UNDEFINED);
551-
552-
String s1 = as1.getSequenceAsString(start, end, Strand.UNDEFINED);
553-
String s2 = as2.getSequenceAsString(start, end, Strand.UNDEFINED);
549+
String mySeq = as.getSubSequence(start, end).getSequenceAsString();
550+
551+
String s1 = as1.getSubSequence(start, end).getSequenceAsString();
552+
String s2 = as2.getSubSequence(start, end).getSequenceAsString();
554553

555554
for ( int i =0 ; i < s1.length(); i++){
556555
if ( i >= s2.length())
@@ -606,8 +605,8 @@ private void printConservation(StringBuilder s, String idFormat,
606605
s.append(String.format("%" + (seqIndexPad + 1) + "s", ""));
607606
}
608607

609-
String subseq1 = as1.getSequenceAsString(start, end, Strand.UNDEFINED);
610-
String subseq2 = as2.getSequenceAsString(start, end, Strand.UNDEFINED);
608+
String subseq1 = as1.getSubSequence(start, end).getSequenceAsString();
609+
String subseq2 = as2.getSubSequence(start, end).getSequenceAsString();
611610

612611
for ( int ii =0 ; ii < subseq1.length() ; ii++){
613612
if ( ii >= subseq2.length())

‎biojava3-alignment/src/test/java/org/biojava3/alignment/SimpleAlignedSequenceTest.java‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -308,9 +308,9 @@ public void testGetSequenceAsString() {
308308

309309
@Test
310310
public void testGetSequenceAsStringIntegerIntegerStrand() {
311-
assertEquals(global.getSequenceAsString(2, 5, Strand.UNDEFINED), "AR-N");
312-
assertEquals(local.getSequenceAsString(2, 6, Strand.UNDEFINED), "Q--G-");
313-
assertEquals(local2.getSequenceAsString(2, 3, Strand.UNDEFINED), "ND");
311+
assertEquals(global.getSubSequence(2, 5).getSequenceAsString(), "AR-N");
312+
assertEquals(local.getSubSequence(2, 6).getSequenceAsString(), "Q--G-");
313+
assertEquals(local2.getSubSequence(2, 3).getSequenceAsString(), "ND");
314314
}
315315

316316
@Ignore // TODO SimpleAlignedSequence.getSubSequence(Integer, Integer)

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