From 20dd6fc13a9d903dc580939e7f2722bc9b043c4f Mon Sep 17 00:00:00 2001 From: gmungoc Date: Fri, 10 Jul 2015 06:16:25 +0100 Subject: [PATCH] JAL-1807 explicit imports (jalview.structure) --- src/jalview/structure/SelectionListener.java | 7 ++- src/jalview/structure/SequenceListener.java | 3 +- .../structure/StructureSelectionManager.java | 54 ++++++++++---------- 3 files changed, 35 insertions(+), 29 deletions(-) diff --git a/src/jalview/structure/SelectionListener.java b/src/jalview/structure/SelectionListener.java index 2877d46..6d9b54c 100644 --- a/src/jalview/structure/SelectionListener.java +++ b/src/jalview/structure/SelectionListener.java @@ -20,6 +20,9 @@ */ package jalview.structure; +import jalview.datamodel.ColumnSelection; +import jalview.datamodel.SequenceGroup; + /** * Implemented by objects listening for selection events on SelectionSources */ @@ -37,6 +40,6 @@ public interface SelectionListener * @param source * - source of the selection event */ - public void selection(jalview.datamodel.SequenceGroup seqsel, - jalview.datamodel.ColumnSelection colsel, SelectionSource source); + public void selection(SequenceGroup seqsel, ColumnSelection colsel, + SelectionSource source); } diff --git a/src/jalview/structure/SequenceListener.java b/src/jalview/structure/SequenceListener.java index cb65032..2be58dd 100644 --- a/src/jalview/structure/SequenceListener.java +++ b/src/jalview/structure/SequenceListener.java @@ -20,6 +20,7 @@ */ package jalview.structure; +import jalview.datamodel.SearchResults; import jalview.datamodel.SequenceI; @@ -28,7 +29,7 @@ public interface SequenceListener // TODO remove this? never called on SequenceListener type public void mouseOverSequence(SequenceI sequence, int index, int pos); - public void highlightSequence(jalview.datamodel.SearchResults results); + public void highlightSequence(SearchResults results); // TODO remove this? never called public void updateColours(SequenceI sequence, int index); diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java index ac14b52..71baaff 100644 --- a/src/jalview/structure/StructureSelectionManager.java +++ b/src/jalview/structure/StructureSelectionManager.java @@ -20,6 +20,26 @@ */ package jalview.structure; +import jalview.analysis.AlignSeq; +import jalview.api.AlignmentViewPanel; +import jalview.api.StructureSelectionManagerProvider; +import jalview.commands.CommandI; +import jalview.commands.EditCommand; +import jalview.commands.OrderCommand; +import jalview.datamodel.AlignedCodonFrame; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.Annotation; +import jalview.datamodel.ColumnSelection; +import jalview.datamodel.Mapping; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.SearchResults; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; +import jalview.io.AppletFormatAdapter; +import jalview.util.MappingUtils; +import jalview.util.MessageManager; + import java.io.PrintStream; import java.util.ArrayList; import java.util.Arrays; @@ -37,22 +57,6 @@ import MCview.Atom; import MCview.PDBChain; import MCview.PDBfile; -import jalview.analysis.AlignSeq; -import jalview.api.StructureSelectionManagerProvider; -import jalview.commands.CommandI; -import jalview.commands.EditCommand; -import jalview.commands.OrderCommand; -import jalview.datamodel.AlignedCodonFrame; -import jalview.datamodel.AlignmentAnnotation; -import jalview.datamodel.AlignmentI; -import jalview.datamodel.Annotation; -import jalview.datamodel.PDBEntry; -import jalview.datamodel.SearchResults; -import jalview.datamodel.SequenceI; -import jalview.io.AppletFormatAdapter; -import jalview.util.MappingUtils; -import jalview.util.MessageManager; - public class StructureSelectionManager { public final static String NEWLINE = System.lineSeparator(); @@ -500,10 +504,8 @@ public class StructureSelectionManager + seq.getEnd() - 1)); maxChain.makeExactMapping(maxAlignseq, seq); - jalview.datamodel.Mapping sqmpping = maxAlignseq - .getMappingFromS1(false); - jalview.datamodel.Mapping omap = new jalview.datamodel.Mapping( - sqmpping.getMap().getInverse()); + Mapping sqmpping = maxAlignseq.getMappingFromS1(false); + Mapping omap = new Mapping(sqmpping.getMap().getInverse()); maxChain.transferRESNUMFeatures(seq, null); // allocate enough slots to store the mapping from positions in @@ -525,7 +527,7 @@ public class StructureSelectionManager index++; } while (index < maxChain.atoms.size()); - if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE)) + if (protocol.equals(AppletFormatAdapter.PASTE)) { pdbFile = "INLINE" + pdb.id; } @@ -827,7 +829,7 @@ public class StructureSelectionManager * "+mappings[j].pdbfile); * * java.awt.Color col; for(int index=0; index 0) { col = sl.getColour(atomNo, @@ -1001,9 +1003,8 @@ public class StructureSelectionManager } } - public synchronized void sendSelection( - jalview.datamodel.SequenceGroup selection, - jalview.datamodel.ColumnSelection colsel, SelectionSource source) + public synchronized void sendSelection(SequenceGroup selection, + ColumnSelection colsel, SelectionSource source) { for (SelectionListener slis : sel_listeners) { @@ -1017,7 +1018,8 @@ public class StructureSelectionManager Vector view_listeners = new Vector(); public synchronized void sendViewPosition( - jalview.api.AlignmentViewPanel source, int startRes, int endRes, +AlignmentViewPanel source, + int startRes, int endRes, int startSeq, int endSeq) { -- 1.7.10.2