From e7543a7264d0cd505a7344b704ce669726c44afc Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Mon, 15 Jun 2015 14:03:07 +0100 Subject: [PATCH] JAL-1775 FileLoader javadoc --- src/jalview/io/FileLoader.java | 20 ++++++++++++-------- 1 file changed, 12 insertions(+), 8 deletions(-) diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java index 76bd572..0cd2987 100755 --- a/src/jalview/io/FileLoader.java +++ b/src/jalview/io/FileLoader.java @@ -20,12 +20,6 @@ */ package jalview.io; -import java.util.StringTokenizer; -import java.util.Vector; - -import javax.swing.JOptionPane; -import javax.swing.SwingUtilities; - import jalview.api.ComplexAlignFile; import jalview.datamodel.AlignmentI; import jalview.datamodel.ColumnSelection; @@ -39,6 +33,12 @@ import jalview.schemes.ColourSchemeI; import jalview.structure.StructureSelectionManager; import jalview.util.MessageManager; +import java.util.StringTokenizer; +import java.util.Vector; + +import javax.swing.JOptionPane; +import javax.swing.SwingUtilities; + public class FileLoader implements Runnable { String file; @@ -317,6 +317,7 @@ public class FileLoader implements Runnable if ((al != null) && (al.getHeight() > 0)) { + // construct and register dataset sequences for (SequenceI sq : al.getSequences()) { while (sq.getDatasetSequence() != null) @@ -327,13 +328,17 @@ public class FileLoader implements Runnable { for (PDBEntry pdbe : sq.getPDBId()) { + // register PDB entries with desktop's structure selection + // manager StructureSelectionManager.getStructureSelectionManager( Desktop.instance).registerPDBEntry(pdbe); } } } + if (viewport != null) { + // append to existing alignment viewport.addAlignment(al, title); } else @@ -351,8 +356,7 @@ public class FileLoader implements Runnable ColourSchemeI cs = ((ComplexAlignFile) source) .getColourScheme(); alignFrame = new AlignFrame(al, hiddenSeqs, colSel, - AlignFrame.DEFAULT_WIDTH, - AlignFrame.DEFAULT_HEIGHT); + AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); alignFrame.getViewport().setShowSequenceFeatures( showSeqFeatures); -- 1.7.10.2