X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructures%2Fmodels%2FAAStructureBindingModel.java;h=9f4cea03736531ce3371e702969eaaea58ae5d8f;hb=bd4ab013e64863bbbffa93c58953051e11cfb236;hp=d9e8c953141bbaf11b394ffd0ed425fcb1fdd932;hpb=865633cd6ddc767e82ac3fd265ac2d9400a25198;p=jalview.git diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java index d9e8c95..9f4cea0 100644 --- a/src/jalview/structures/models/AAStructureBindingModel.java +++ b/src/jalview/structures/models/AAStructureBindingModel.java @@ -25,7 +25,7 @@ import jalview.api.SequenceRenderer; import jalview.api.StructureSelectionManagerProvider; import jalview.api.structures.JalviewStructureDisplayI; import jalview.datamodel.AlignmentI; -import jalview.datamodel.ColumnSelection; +import jalview.datamodel.HiddenColumns; import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; import jalview.io.DataSourceType; @@ -53,9 +53,9 @@ import java.util.List; * @author gmcarstairs * */ -public abstract class AAStructureBindingModel extends - SequenceStructureBindingModel implements StructureListener, - StructureSelectionManagerProvider +public abstract class AAStructureBindingModel + extends SequenceStructureBindingModel + implements StructureListener, StructureSelectionManagerProvider { private StructureSelectionManager ssm; @@ -300,7 +300,8 @@ public abstract class AAStructureBindingModel extends { throw new Error(MessageManager.formatMessage( "error.implementation_error_no_pdbentry_from_index", - new Object[] { Integer.valueOf(pe).toString() })); + new Object[] + { Integer.valueOf(pe).toString() })); } final String nullChain = "TheNullChain"; List s = new ArrayList(); @@ -638,8 +639,8 @@ public abstract class AAStructureBindingModel extends if (waiting) { - System.err - .println("Timed out waiting for structure viewer to load file " + System.err.println( + "Timed out waiting for structure viewer to load file " + notLoaded); return false; } @@ -657,10 +658,8 @@ public abstract class AAStructureBindingModel extends { for (SequenceI s : seqs) { - if (s == seq - || (s.getDatasetSequence() != null && s - .getDatasetSequence() == seq - .getDatasetSequence())) + if (s == seq || (s.getDatasetSequence() != null + && s.getDatasetSequence() == seq.getDatasetSequence())) { return true; } @@ -716,8 +715,8 @@ public abstract class AAStructureBindingModel extends * an array of corresponding hidden columns for each alignment * @return */ - public abstract String superposeStructures(AlignmentI[] alignments, int[] structureIndices, - ColumnSelection[] hiddenCols); + public abstract String superposeStructures(AlignmentI[] alignments, + int[] structureIndices, HiddenColumns[] hiddenCols); public abstract void setBackgroundColour(Color col); @@ -732,7 +731,8 @@ public abstract class AAStructureBindingModel extends * * @return */ - public abstract SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment); + public abstract SequenceRenderer getSequenceRenderer( + AlignmentViewPanel alignment); protected abstract void colourBySequence( StructureMappingcommandSet[] colourBySequenceCommands); @@ -757,9 +757,9 @@ public abstract class AAStructureBindingModel extends return; } String[] files = getStructureFiles(); - + SequenceRenderer sr = getSequenceRenderer(alignmentv); - + StructureMappingcommandSet[] colourBySequenceCommands = getColourBySequenceCommands( files, sr, alignmentv); colourBySequence(colourBySequenceCommands);