JAL-1665 getSequenceFeatures; Desktop.getAlignFrames camel-cased

diff --git a/examples/groovy/alignLoadedFile.groovy b/examples/groovy/alignLoadedFile.groovy
index 6d8f807..681a090 100644 (file)
--- 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 (file)
--- 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 (file)
--- 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 (file)
--- 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 (file)
--- 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 (file)
--- 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 (file)
--- 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 (file)
--- 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 (file)
--- 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 (file)
--- 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 (file)
--- 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