{
AlignedCodonFrame acf1 = new AlignedCodonFrame();
acf1.addMap(new Sequence("s1", "ttt"), new Sequence("p1", "p"),
- new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1));
+ new MapList(new int[]
+ { 1, 3 }, new int[] { 1, 1 }, 1, 1));
AlignedCodonFrame acf2 = new AlignedCodonFrame();
acf2.addMap(new Sequence("s2", "ttt"), new Sequence("p2", "p"),
- new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1));
+ new MapList(new int[]
+ { 1, 3 }, new int[] { 1, 1 }, 1, 1));
ssm.registerMapping(acf1);
assertEquals(1, ssm.getSequenceMappings().size());
{
AlignedCodonFrame acf1 = new AlignedCodonFrame();
acf1.addMap(new Sequence("s1", "ttt"), new Sequence("p1", "p"),
- new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1));
+ new MapList(new int[]
+ { 1, 3 }, new int[] { 1, 1 }, 1, 1));
AlignedCodonFrame acf2 = new AlignedCodonFrame();
acf2.addMap(new Sequence("s2", "ttt"), new Sequence("p2", "p"),
- new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1));
+ new MapList(new int[]
+ { 1, 3 }, new int[] { 1, 1 }, 1, 1));
AlignedCodonFrame acf3 = new AlignedCodonFrame();
acf3.addMap(new Sequence("s3", "ttt"), new Sequence("p3", "p"),
- new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1));
+ new MapList(new int[]
+ { 1, 3 }, new int[] { 1, 1 }, 1, 1));
List<AlignedCodonFrame> set1 = new ArrayList<>();
set1.add(acf1);
@Test(groups = { "Functional" })
public void testSetMapping_seqFeatures()
{
- SequenceI seq = new Sequence(
- "1GAQ|B",
+ SequenceI seq = new Sequence("1GAQ|B",
"ATYNVKLITPEGEVELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDVVIETHKEEELTGA");
StructureSelectionManager sm = new StructureSelectionManager();
sm.setProcessSecondaryStructure(true);
sm.setAddTempFacAnnot(true);
StructureFile pmap = sm.setMapping(true, new SequenceI[] { seq },
- new String[] { null }, "examples/1gaq.txt", DataSourceType.FILE);
+ new String[]
+ { null }, "examples/1gaq.txt", DataSourceType.FILE);
assertTrue(pmap != null);
assertEquals(3, pmap.getSeqs().size());
// for some reason 'BeforeMethod' (which should be inherited from
// Jalview2XmlBase isn't always called)...
Desktop.instance.closeAll_actionPerformed(null);
- try {
+ try
+ {
Thread.sleep(200);
- } catch (Exception foo) {};
+ } catch (Exception foo)
+ {
+ }
+ ;
SequenceI seq = new Sequence("4IM2|A",
"LDFCIRNIEKTVMGEISDIHTKLLRLSSSQGTIE");
String P4IM2_MISSING = "examples/testdata/4IM2_missing.pdb";
sm.setAddTempFacAnnot(true);
StructureFile pmap = sm.setMapping(true, new SequenceI[] { seq },
new String[]
- { null }, P4IM2_MISSING,
- DataSourceType.FILE);
+ { null }, P4IM2_MISSING, DataSourceType.FILE);
assertTrue(pmap != null);
assertEquals(1, pmap.getSeqs().size());
// alignment
verifySeqFeats(pdb_viewseq, offset, fdesc);
-
JalviewStructureDisplayI viewr = openStructureViaChooser(alf,
pdb_viewseq, "4IM2");
PDBEntry pdbe = seq.getPDBEntry("4IM2");
StructureSelectionManager apssm = alf.alignPanel
.getStructureSelectionManager();
- StructureMapping[] smap = apssm
- .getMapping(pdbe.getFile());
+ StructureMapping[] smap = apssm.getMapping(pdbe.getFile());
assertNotNull(smap);
assertNotNull(smap[0]);
// find the last position in the alignment sequence - this is not
{ pdbe.getFile() },
new SequenceI[][]
{ new SequenceI[] { pdb_viewseq } },
- new SequenceRenderer(alf.alignPanel.getAlignViewport()),
- alf.alignPanel);
+ new SequenceRenderer(alf.alignPanel.getAlignViewport()),
+ alf.alignPanel);
// Expected - all residues are white
for (String c : smcr)
{
// currently this test fails if trimming is enabled
Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
Boolean.FALSE.toString());
- String TEMP_FACTOR_AA="Temperature Factor";
+ String TEMP_FACTOR_AA = "Temperature Factor";
String PDBID = "4IM2";
- String FullLengthSeq = ">TBK1_HUMAN Serine/threonine-protein kinase TBK1\n" +
- "MQSTSNHLWLLSDILGQGATANVFRGRHKKTGDLFAIKVFNNISFLRPVDVQMREFEVLKKLNHKNIVKLFA\n" +
- "IEEETTTRHKVLIMEFCPCGSLYTVLEEPSNAYGLPESEFLIVLRDVVGGMNHLRENGIVHRDIKPGNIMRV\n" +
- "IGEDGQSVYKLTDFGAARELEDDEQFVSLYGTEEYLHPDMYERAVLRKDHQKKYGATVDLWSIGVTFYHAAT\n" +
- "GSLPFRPFEGPRRNKEVMYKIITGKPSGAISGVQKAENGPIDWSGDMPVSCSLSRGLQVLLTPVLANILEAD\n" +
- "QEKCWGFDQFFAETSDILHRMVIHVFSLQQMTAHKIYIHSYNTATIFHELVYKQTKIISSNQELIYEGRRLV\n" +
- "LEPGRLAQHFPKTTEENPIFVVSREPLNTIGLIYEKISLPKVHPRYDLDGDASMAKAITGVVCYACRIASTL\n" +
- "LLYQELMRKGIRWLIELIKDDYNETVHKKTEVVITLDFCIRNIEKTVKVYEKLMKINLEAAELGEISDIHTK\n" +
- "LLRLSSSQGTIETSLQDIDSRLSPGGSLADAWAHQEGTHPKDRNVEKLQVLLNCMTEIYYQFKKDKAERRLA\n" +
- "YNEEQIHKFDKQKLYYHATKAMTHFTDECVKKYEAFLNKSEEWIRKMLHLRKQLLSLTNQCFDIEEEVSKYQ\n" +
- "EYTNELQETLPQKMFTASSGIKHTMTPIYPSSNTLVEMTLGMKKLKEEMEGVVKELAENNHILERFGSLTMD\n" +
- "GGLRNVDCL";
+ String FullLengthSeq = ">TBK1_HUMAN Serine/threonine-protein kinase TBK1\n"
+ + "MQSTSNHLWLLSDILGQGATANVFRGRHKKTGDLFAIKVFNNISFLRPVDVQMREFEVLKKLNHKNIVKLFA\n"
+ + "IEEETTTRHKVLIMEFCPCGSLYTVLEEPSNAYGLPESEFLIVLRDVVGGMNHLRENGIVHRDIKPGNIMRV\n"
+ + "IGEDGQSVYKLTDFGAARELEDDEQFVSLYGTEEYLHPDMYERAVLRKDHQKKYGATVDLWSIGVTFYHAAT\n"
+ + "GSLPFRPFEGPRRNKEVMYKIITGKPSGAISGVQKAENGPIDWSGDMPVSCSLSRGLQVLLTPVLANILEAD\n"
+ + "QEKCWGFDQFFAETSDILHRMVIHVFSLQQMTAHKIYIHSYNTATIFHELVYKQTKIISSNQELIYEGRRLV\n"
+ + "LEPGRLAQHFPKTTEENPIFVVSREPLNTIGLIYEKISLPKVHPRYDLDGDASMAKAITGVVCYACRIASTL\n"
+ + "LLYQELMRKGIRWLIELIKDDYNETVHKKTEVVITLDFCIRNIEKTVKVYEKLMKINLEAAELGEISDIHTK\n"
+ + "LLRLSSSQGTIETSLQDIDSRLSPGGSLADAWAHQEGTHPKDRNVEKLQVLLNCMTEIYYQFKKDKAERRLA\n"
+ + "YNEEQIHKFDKQKLYYHATKAMTHFTDECVKKYEAFLNKSEEWIRKMLHLRKQLLSLTNQCFDIEEEVSKYQ\n"
+ + "EYTNELQETLPQKMFTASSGIKHTMTPIYPSSNTLVEMTLGMKKLKEEMEGVVKELAENNHILERFGSLTMD\n"
+ + "GGLRNVDCL";
/*
* annotation exported after importing full length sequence to desktop, opening 4IM2 and selecting 'Add Reference Annotation'.
*
* Note - tabs must be replaced with \t - Eclipse expands them to spaces otherwise.
*/
- String FullLengthAnnot = "JALVIEW_ANNOTATION\n" +
- "# Created: Mon Feb 05 15:30:20 GMT 2018\n" +
- "# Updated: Fri Feb 09 17:05:17 GMT 2018\n" +
- "\n" +
- "\n" +
- "SEQUENCE_REF\tTBK1_HUMAN\n"
+ String FullLengthAnnot = "JALVIEW_ANNOTATION\n"
+ + "# Created: Mon Feb 05 15:30:20 GMT 2018\n"
+ + "# Updated: Fri Feb 09 17:05:17 GMT 2018\n" + "\n" + "\n"
+ + "SEQUENCE_REF\tTBK1_HUMAN\n"
+ "LINE_GRAPH\tTemperature Factor\tTemperature Factor for 4im2A\t125.22|128.51|120.35|113.12|122.6|114.44|91.49|102.53|98.22|111.41|111.32|116.64|103.55|100.53|95.07|105.55|114.76|128.29|133.55|142.14|121.12|110.36|95.79|95.39|87.14|99.56|93.55|94.21|100.33|110.68|97.85|82.37|75.87|76.53|77.85|82.49|80.92|96.88|122.58|133.31|160.15|180.51|||||242.88|258.97|247.01|227.12|223.24|211.62|184.65|183.51|168.96|160.04|150.88|131.68|130.43|139.87|148.59|136.57|125.7|96.51|74.49|74.08|85.87|70.93|86.47|101.59|97.51|97.39|117.19|114.27|129.5|112.98|147.52|170.26|154.98|168.18|157.51|131.95|105.85|97.78|97.35|76.51|76.31|72.55|71.43|78.82|79.94|75.04|79.54|77.95|83.56|88.5|71.51|71.73|75.96|82.36|81.75|66.51|67.23|69.35|67.92|54.75|71.19|61.85|65.34|67.97|64.51|67.41|62.28|72.85|72.76|70.64|65.23|71.07|67.73|87.72|64.93|75.92|94.02|99.35|93.71|103.59|106.29|115.46|118.69|147.18|130.62|171.64|158.95|164.11||107.42|88.53|83.52|88.06|94.06|80.82|59.01|59.73|78.89|69.21|70.34|81.95|74.53|60.92|64.65|55.79|75.71|68.86|70.95|75.08|87.76|85.43|105.84|||||||||||||||||137.46|151.33|145.17|122.79|111.56|126.72|124.06|161.75|176.84|180.51|198.49|196.75|187.41||195.23|202.27|203.16|226.55|221.75|193.83||||||172.33|177.97|151.47|132.65|99.22|93.7|91.15|88.24|72.35|70.05|70.0|74.92|66.51|68.37|65.76|70.12|74.97|76.89|80.83|70.21|69.48|79.54|82.65|96.54|114.31|140.46|168.51|176.99|205.08|209.27|155.83|139.41|151.3|129.33|111.31|119.62|121.37|102.26|115.39|129.97|128.65|110.38|110.66|116.1|82.53|84.02|82.17|87.63|86.42|77.23|91.23|95.53|102.21|120.73|133.26|109.67|108.49|93.25|92.85|86.39|95.66|94.92|85.82|80.13|76.17|86.61|78.9|77.97|105.6|70.66|69.35|78.94|66.68|63.03|69.91|79.05|75.43|70.73|70.02|80.57|81.74|77.99|84.1|91.66|92.42|94.03|116.47|132.01|154.55|163.99|161.37|155.23|132.78|109.3|90.38|101.83|99.61|91.68|82.77|86.12|82.73|90.13|85.14|79.54|74.27|74.06|72.88|86.34|72.0|69.32|60.9|68.15|52.99|63.53|61.3|66.01|68.28|77.41|71.52|67.18|66.17|71.51|65.47|52.63|65.08|66.37|73.76|77.79|67.58|79.53|84.75|87.42|78.9|79.19|85.57|73.67|80.56|86.19|72.17|66.27|72.8|86.28|78.89|74.5|90.6|80.42|92.5|92.84|96.18|92.08|88.5|87.25|64.6|68.95|65.56|67.55|71.62|78.24|84.95|71.35|86.41|84.73|94.41|95.09|84.74|87.64|88.85|75.1|86.42|79.28|73.14|78.54|80.81|60.66|67.93|71.64|59.85|64.7|61.22|63.84|65.9|62.18|74.95|72.92|93.37|90.47|96.0|93.8|88.46|79.78|83.4|66.55|68.7|73.2|78.76|85.67|84.8|89.59|96.52|79.53|103.51|134.72|126.7|145.31|156.17|149.35|128.48|117.29|118.98|131.59|109.36|90.39|87.68|91.81|78.77|80.11|91.39|75.57|78.98|71.53|76.85|70.9|64.71|73.55|73.45|60.0|69.92|57.89|69.07|66.45|62.85|57.83|57.89|66.4|61.61|60.85|66.47|63.53|63.84|65.96|73.06|70.82|64.51|63.66|73.37|73.59|68.09|78.93|76.99|75.05|71.32|88.4|78.88|93.08|110.61|94.32|99.24|128.99|129.49|132.74|124.21|120.32|142.06|166.41|149.87|153.29|172.19|165.89|181.6|223.11|237.73|176.41|171.09|189.65|188.61|154.84|142.72|154.25|170.99|175.65|||||||110.61||||||||||158.07|170.73|167.93|198.47|212.36|181.71|157.69|163.31|138.96|120.29|131.63|152.26|125.06|136.66|148.97|129.68|120.52|135.31|136.05|119.39|124.18|128.94|123.02|103.37|128.44|134.12|118.88|120.94|130.38|124.67|112.21|113.69|123.65|132.06|114.97|110.75|92.38|101.2|103.25|94.84|85.3|82.19|89.81|98.81|83.03|68.91|65.24|70.31|63.49|86.38|71.07|62.65|63.95|66.98|58.06|68.28|62.11|63.86|67.4|68.69|69.57|68.03|74.23|75.66|70.67|81.08|81.31|82.49|88.15|95.99|92.97|100.01|113.18|122.37|110.99|122.19|159.27|147.74|133.96|111.2|115.64|126.55|107.15|102.85|117.06|116.56|109.55|96.82|98.92|96.53|86.0|88.11|92.76|85.77|79.41|93.06|86.96|76.35|72.37|74.19|68.6|67.46|74.47|76.25|66.73|73.18|75.2|88.21|84.93|75.04|71.09|82.6|80.03|76.22|75.76|83.72|75.85|79.36|90.35|86.9|78.24|95.64|97.38|86.41|85.02|91.87|87.36|77.56|81.25|91.66|83.65|77.67|85.07|89.21|92.66|92.46|89.0|100.83|96.71|94.81|101.37|111.28|124.48|119.73|127.81|134.41|132.4|140.32|140.86|166.52|160.16|168.39|176.74|174.63|172.86|168.55|155.9|132.71|113.44|113.49|123.9|151.11|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n"
- +
- "\n" +
- "";
- AlignFrame alf_full=new
- FileLoader(false).LoadFileWaitTillLoaded(FullLengthSeq,DataSourceType.PASTE);
- alf_full.loadJalviewDataFile(FullLengthAnnot, DataSourceType.PASTE, null, null);
+ + "\n" + "";
+ AlignFrame alf_full = new FileLoader(false)
+ .LoadFileWaitTillLoaded(FullLengthSeq, DataSourceType.PASTE);
+ alf_full.loadJalviewDataFile(FullLengthAnnot, DataSourceType.PASTE,
+ null, null);
AlignmentI al_full = alf_full.getViewport().getAlignment();
- AlignmentAnnotation fullseq_tf = al_full.findAnnotations(al_full.getSequences().get(0), null, TEMP_FACTOR_AA).iterator()
- .next();
+ AlignmentAnnotation fullseq_tf = al_full
+ .findAnnotations(al_full.getSequences().get(0), null,
+ TEMP_FACTOR_AA)
+ .iterator().next();
assertNotNull(fullseq_tf);
-
+
// getMappingFor
// AlignmentI al_full=alf_full.getViewport().getAlignment();
//
JalviewStructureDisplayI sview = openStructureViaChooser(alf, seq,
PDBID);
- AlignmentAnnotation subseq_tf=null;
+ AlignmentAnnotation subseq_tf = null;
assertTrue(seq.getDBRefs() != null && seq.getDBRefs().size() > 0);
-
+
if (!al.findAnnotations(seq, null, TEMP_FACTOR_AA).iterator().hasNext())
{
// FIXME JAL-2321 - don't see reference annotation on alignment the first
// verify location of secondary structure annotation
// Specific positions: LYS477 (h),THR478 (no helix), ... GLY496(no helix),
// GLU497 (helix),
-
+
// check there is or is not a tempfactor for each mapped position, and that
// values are equal for those positions.
- for (int p=seq.getStart();p<=seq.getEnd();p++)
+ for (int p = seq.getStart(); p <= seq.getEnd(); p++)
{
- Annotation orig,subseq;
+ Annotation orig, subseq;
orig = fullseq_tf.getAnnotationForPosition(p);
subseq = subseq_tf.getAnnotationForPosition(p);
if (orig == null)
}
private JalviewStructureDisplayI openStructureViaChooser(AlignFrame alf,
- SequenceI seq,
- String pDBID)
+ SequenceI seq, String pDBID)
{
SequenceI[] selectedSeqs = new SequenceI[] { seq };
git://source.jalview.org / jalview.git / blobdiff