From: gmungoc Date: Thu, 26 Mar 2015 09:52:09 +0000 (+0000) Subject: JAL-1665 getSequenceFeatures; Desktop.getAlignFrames camel-cased X-Git-Tag: Jalview_2_9~73^2~2 X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=89cb45bd28a34f30e807efe12552268e3b5628b8 JAL-1665 getSequenceFeatures; Desktop.getAlignFrames camel-cased --- diff --git a/examples/groovy/alignLoadedFile.groovy b/examples/groovy/alignLoadedFile.groovy index 6d8f807..681a090 100644 --- a/examples/groovy/alignLoadedFile.groovy +++ b/examples/groovy/alignLoadedFile.groovy @@ -23,7 +23,7 @@ if (service.serviceType.indexOf("uscle")>-1) { } catch (q) { // currentAlFrame is not defined - so we were run as an interactive script from the Groovy console // in that case, just pick the first alignmentFrame in the stack. - msaf = Jalview.getAlignframes()[0] + msaf = Jalview.getAlignFrames()[0] }; // Finally start Jalview's JabaWS MSA Client with the alignment from msaf new MsaWSClient(service, msaf.getTitle(), msaf.gatherSequencesForAlignment(), false, diff --git a/examples/groovy/annotationForSelectedSequence.groovy b/examples/groovy/annotationForSelectedSequence.groovy index f071beb..c9e8563 100644 --- a/examples/groovy/annotationForSelectedSequence.groovy +++ b/examples/groovy/annotationForSelectedSequence.groovy @@ -11,7 +11,7 @@ import java.awt.datatransfer.StringSelection import static java.awt.Toolkit.* -def curviewport = Jalview.getAlignframes()[Jalview.getAlignframes().length-1].getViewport(); +def curviewport = Jalview.getAlignFrames()[Jalview.getAlignFrames().length-1].getViewport(); // TSV output by default. // change "\t" to "," to output CSV file diff --git a/examples/groovy/annotationsascsv.groovy b/examples/groovy/annotationsascsv.groovy index 5f0a66a..b63c2c3 100644 --- a/examples/groovy/annotationsascsv.groovy +++ b/examples/groovy/annotationsascsv.groovy @@ -1,6 +1,6 @@ // do something groovy in jalview print "Hello World.\n"; -def alf = Jalview.getAlignframes(); +def alf = Jalview.getAlignFrames(); for (ala in alf) { def alignment = ala.viewport.alignment; diff --git a/examples/groovy/closures.groovy b/examples/groovy/closures.groovy index 9e4dd52..eaa84e3 100644 --- a/examples/groovy/closures.groovy +++ b/examples/groovy/closures.groovy @@ -1,5 +1,5 @@ writeAnnot = { - new File(it).append(new jalview.io.AnnotationFile().printAnnotations(Jalview.getAlignframes()[0].getViewport().getAlignment().getAlignmentAnnotation(),null,null)) + new File(it).append(new jalview.io.AnnotationFile().printAnnotations(Jalview.getAlignFrames()[0].getViewport().getAlignment().getAlignmentAnnotation(),null,null)) } diff --git a/examples/groovy/iterateOverAlignments.groovy b/examples/groovy/iterateOverAlignments.groovy index 83c4169..dbca845 100644 --- a/examples/groovy/iterateOverAlignments.groovy +++ b/examples/groovy/iterateOverAlignments.groovy @@ -3,7 +3,7 @@ import jalview.datamodel.*; import jalview.gui.AlignFrame; import jalview.gui.AlignViewport; -def af = Jalview.getAlignframes(); +def af = Jalview.getAlignFrames(); for (ala in af) { diff --git a/examples/groovy/parseproperties.groovy b/examples/groovy/parseproperties.groovy index 646ebf8..c011698 100644 --- a/examples/groovy/parseproperties.groovy +++ b/examples/groovy/parseproperties.groovy @@ -3,7 +3,7 @@ import jalview.datamodel.*; import jalview.gui.AlignFrame; import jalview.gui.AlignViewport; -def af = Jalview.getAlignframes(); +def af = Jalview.getAlignFrames(); def al = af[0].viewport.alignment; ParseProperties pp = new ParseProperties(al); pp.getScoresFromDescription("Score", "ScanPS Raw Score", "([-0-9.+]+)"); diff --git a/examples/groovy/printtitle.groovy b/examples/groovy/printtitle.groovy index 5a2166d..0d462f1 100644 --- a/examples/groovy/printtitle.groovy +++ b/examples/groovy/printtitle.groovy @@ -1,6 +1,6 @@ // do something groovy in jalview print "Hello World.\n"; -def alf = Jalview.getAlignframes(); +def alf = Jalview.getAlignFrames(); for (ala in alf) { // ala is an jalview.gui.AlignFrame object diff --git a/examples/groovy/removeFeaturesByGroup.groovy b/examples/groovy/removeFeaturesByGroup.groovy index bf7f74d..34a8c94 100644 --- a/examples/groovy/removeFeaturesByGroup.groovy +++ b/examples/groovy/removeFeaturesByGroup.groovy @@ -3,7 +3,7 @@ import jalview.datamodel.*; import jalview.gui.AlignFrame; import jalview.gui.AlignViewport; -def af = Jalview.getAlignframes(); +def af = Jalview.getAlignFrames(); def todie = "PDBFile"; // about to delete this type of group for (ala in af) diff --git a/examples/groovy/selectColumnsByFeatureAndGroup.groovy b/examples/groovy/selectColumnsByFeatureAndGroup.groovy index 0a16391..ea2c596 100644 --- a/examples/groovy/selectColumnsByFeatureAndGroup.groovy +++ b/examples/groovy/selectColumnsByFeatureAndGroup.groovy @@ -11,7 +11,7 @@ def nal=0; def nfeat=0; def nseq=0; -for (ala in Jalview.getAlignframes()) { +for (ala in Jalview.getAlignFrames()) { def al = ala.viewport.alignment; if (al!=null) { @@ -21,7 +21,7 @@ for (ala in Jalview.getAlignframes()) { { def tfeat=0; if (sq!=null) { - SequenceFeature[] sf = sq.getDatasetSequence().getSequenceFeatures(); + SequenceFeature[] sf = sq.getSequenceFeatures(); for (sfpos in sf) { if (sfpos!=null && sfpos.getType().equals(toselect)) diff --git a/examples/groovy/sitesForSelectedColumns.groovy b/examples/groovy/sitesForSelectedColumns.groovy index f84bc93..4f68ed8 100644 --- a/examples/groovy/sitesForSelectedColumns.groovy +++ b/examples/groovy/sitesForSelectedColumns.groovy @@ -9,7 +9,7 @@ import java.awt.datatransfer.StringSelection import static java.awt.Toolkit.* -def curviewport = Jalview.getAlignframes()[Jalview.getAlignframes().length-1].getViewport() +def curviewport = Jalview.getAlignFrames()[Jalview.getAlignFrames().length-1].getViewport() def debug = false diff --git a/examples/groovy/stripUniprotPrefixes.groovy b/examples/groovy/stripUniprotPrefixes.groovy index e2bb129..284d0cf 100644 --- a/examples/groovy/stripUniprotPrefixes.groovy +++ b/examples/groovy/stripUniprotPrefixes.groovy @@ -3,7 +3,7 @@ import jalview.datamodel.*; import jalview.gui.AlignFrame; import jalview.gui.AlignViewport; -def af = Jalview.getAlignframes(); +def af = Jalview.getAlignFrames(); // walk through all alignments, stripping off all text prior to and including last '|' symbol in sequence IDs