X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalviewAppLoader.java;fp=src%2Fjalview%2Fbin%2FJalviewAppLoader.java;h=0000000000000000000000000000000000000000;hb=4f77328104498504339216829abf5ea87e2791ec;hp=51a03306e46382c3ac1221666481852f98dacdf0;hpb=2b8c0785318a3528e1876e8e2dd48b7d831eae69;p=jalview.git
diff --git a/src/jalview/bin/JalviewAppLoader.java b/src/jalview/bin/JalviewAppLoader.java
deleted file mode 100644
index 51a0330..0000000
--- a/src/jalview/bin/JalviewAppLoader.java
+++ /dev/null
@@ -1,1483 +0,0 @@
-package jalview.bin;
-
-import jalview.api.AlignFrameI;
-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;
-import java.util.StringTokenizer;
-import java.util.Vector;
-
-/**
- * A class to load parameters for either JalviewLite or Jalview
- *
- * @author hansonr
- *
- */
-public class JalviewAppLoader
-{
-
- private JalviewApp app; // Jalview or JalviewJS or JalviewLite
-
- private boolean debug;
-
- 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)
- {
- this.debug = debug;
- }
-
- public void load(JalviewApp app)
- {
-
- this.app = app;
-
- String sep = app.getParameter("separator");
- if (sep != null)
- {
- if (sep.length() > 0)
- {
- separator = sep;
- }
- else
- {
- throw new Error(MessageManager
- .getString("error.invalid_separator_parameter"));
- }
- }
-
- loadTree();
- loadScoreFile();
- loadFeatures();
- loadAnnotations();
- loadJnetFile();
- loadPdbFiles();
- callInitCallback();
- }
-
- /**
- * Load PDBFiles if any specified by parameter(s). Returns true if loaded,
- * else false.
- *
- * @param loaderFrame
- * @return
- */
- protected boolean loadPdbFiles()
- {
- boolean result = false;
- /*
- * Undocumented for 2.6 -
- * related to JAL-434
- */
-
- boolean doAlign = app.getDefaultParameter("alignpdbfiles", false);
- app.setAlignPdbStructures(doAlign);
- /*
- *
- *
- *
- *
- *
- */
-
- // Accumulate pdbs here if they are heading for the same view (if
- // alignPdbStructures is true)
- Vector