X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fbin%2FJalviewAppLoader.java;h=a7c504248b69cdef961afd649924aea414c10f99;hb=8e98fa5a09e06ac59c965d030ed71b0158178a24;hp=194d6191eda7b7421bb28aa9ff5d734a83b263ef;hpb=f6a84063f10ea1ae9898310c541961cd1d53dd8a;p=jalview.git
diff --git a/src/jalview/bin/JalviewAppLoader.java b/src/jalview/bin/JalviewAppLoader.java
index 194d619..a7c5042 100644
--- a/src/jalview/bin/JalviewAppLoader.java
+++ b/src/jalview/bin/JalviewAppLoader.java
@@ -2,18 +2,36 @@ package jalview.bin;
import jalview.api.JalviewApp;
import jalview.api.StructureSelectionManagerProvider;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentOrder;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.AlignViewport;
+import jalview.gui.Desktop;
import jalview.io.AnnotationFile;
+import jalview.io.AppletFormatAdapter;
import jalview.io.DataSourceType;
+import jalview.io.FeaturesFile;
+import jalview.io.FileFormat;
+import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
+import jalview.io.IdentifyFile;
import jalview.io.JPredFile;
import jalview.io.JnetAnnotationMaker;
import jalview.io.NewickFile;
+import jalview.structure.SelectionSource;
import jalview.structure.StructureSelectionManager;
import jalview.util.HttpUtils;
import jalview.util.MessageManager;
+import java.awt.EventQueue;
+import java.io.IOException;
import java.net.URL;
import java.util.ArrayList;
import java.util.List;
@@ -29,11 +47,23 @@ import java.util.Vector;
public class JalviewAppLoader
{
- private JalviewApp app;
+ private JalviewApp app; // Jalview or JalviewJS or JalviewLite
private boolean debug;
- private String separator;
+ String separator = "\u00AC"; // JalviewLite note: the default used to
+ // be '|', but many sequence IDS include
+ // pipes.
+
+ public String getSeparator()
+ {
+ return separator;
+ }
+
+ public void setSeparator(String separator)
+ {
+ this.separator = separator;
+ }
public JalviewAppLoader(boolean debug)
{
@@ -65,6 +95,7 @@ public class JalviewAppLoader
loadAnnotations();
loadJnetFile();
loadPdbFiles();
+ callInitCallback();
}
/**
@@ -93,7 +124,6 @@ public class JalviewAppLoader
*
*/
- int pdbFileCount = 0;
// Accumulate pdbs here if they are heading for the same view (if
// alignPdbStructures is true)
Vector