import jalview.schemes.TurnColourScheme;
import jalview.schemes.UserColourScheme;
import jalview.schemes.ZappoColourScheme;
-import jalview.ws.WSMenuEntryProviderI;
import jalview.ws.jws1.Discoverer;
import jalview.ws.jws2.Jws2Discoverer;
+import jalview.ws.seqfetcher.DbSourceProxy;
import java.awt.BorderLayout;
import java.awt.Color;
import java.util.ArrayList;
import java.util.Enumeration;
import java.util.Hashtable;
+import java.util.List;
import java.util.Vector;
import javax.swing.JButton;
wsmenu.add(secstrmenu);
wsmenu.add(dismenu);
wsmenu.add(analymenu);
-// final ArrayList<JMenu> submens=new ArrayList<JMenu>();
-// submens.add(msawsmenu);
- // submens.add(secstrmenu);
- // submens.add(dismenu);
- // submens.add(analymenu);
-
+ // final ArrayList<JMenu> submens=new ArrayList<JMenu>();
+ // submens.add(msawsmenu);
+ // submens.add(secstrmenu);
+ // submens.add(dismenu);
+ // submens.add(analymenu);
+
// No search services yet
// wsmenu.add(seqsrchmenu);
{
final jalview.ws.SequenceFetcher sf = SequenceFetcher
.getSequenceFetcherSingleton(me);
- final String[] otherdb = sf.getOrderedSupportedSources();
- // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
- // jalview.util.QuickSort.sort(otherdb, otherdb);
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
public void run()
{
-
+ String[] dbclasses = sf.getOrderedSupportedSources();
+ // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
+ // jalview.util.QuickSort.sort(otherdb, otherdb);
+ List<DbSourceProxy> otherdb;
JMenu dfetch = new JMenu();
- JMenuItem fetchr;
- rfetch.add(dfetch);
- int comp = 0, mcomp = 15;
+ JMenu ifetch = new JMenu();
+ JMenuItem fetchr = null;
+ int comp = 0, icomp = 0, mcomp = 15;
String mname = null;
- if (otherdb != null && otherdb.length > 0)
+ int dbi = 0;
+ for (String dbclass : dbclasses)
{
- for (int i = 0; i < otherdb.length; i++)
+ otherdb = sf.getSourceProxy(dbclass);
+ // add a single entry for this class, or submenu allowing 'fetch
+ // all' or pick one
+ if (otherdb == null || otherdb.size() < 1)
{
- String dbname = sf.getSourceProxy(otherdb[i]).get(0).getDbName();
- if (mname == null)
- {
- mname = "from '" + dbname + "'";
- }
- fetchr = new JMenuItem(otherdb[i]);
- final String[] dassource = new String[]
- { otherdb[i] };
+ continue;
+ }
+ // List<DbSourceProxy> dbs=otherdb;
+ // otherdb=new ArrayList<DbSourceProxy>();
+ // for (DbSourceProxy db:dbs)
+ // {
+ // if (!db.isA(DBRefSource.ALIGNMENTDB)
+ // }
+ if (mname == null)
+ {
+ mname = "From " + dbclass;
+ }
+ if (otherdb.size() == 1)
+ {
+ final DbSourceProxy[] dassource = otherdb
+ .toArray(new DbSourceProxy[0]);
+ DbSourceProxy src = otherdb.get(0);
+ fetchr = new JMenuItem(src.getDbSource());
fetchr.addActionListener(new ActionListener()
{
}
});
- fetchr.setToolTipText("Retrieve from " + dbname);
+ fetchr.setToolTipText("<html>"
+ + JvSwingUtils.wrapTooltip("Retrieve from "
+ + src.getDbName()) + "<html>");
+ dfetch.add(fetchr);
+ comp++;
+ }
+ else
+ {
+ final DbSourceProxy[] dassource = otherdb
+ .toArray(new DbSourceProxy[0]);
+ // fetch all entry
+ DbSourceProxy src = otherdb.get(0);
+ fetchr = new JMenuItem("Fetch All '" + src.getDbSource()
+ + "'");
+ fetchr.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ new Thread(new Runnable()
+ {
+
+ public void run()
+ {
+ new jalview.ws.DBRefFetcher(alignPanel.av
+ .getSequenceSelection(),
+ alignPanel.alignFrame, dassource)
+ .fetchDBRefs(false);
+ }
+ }).start();
+ }
+ });
+
+ fetchr.setToolTipText("<html>"
+ + JvSwingUtils.wrapTooltip("Retrieve from all "
+ + otherdb.size() + " sources in "
+ + src.getDbSource() + "<br>First is :"
+ + src.getDbName()) + "<html>");
dfetch.add(fetchr);
- if (comp++ == mcomp || i == (otherdb.length - 1))
+ comp++;
+ // and then build the rest of the individual menus
+ ifetch = new JMenu("Sources from " + src.getDbSource());
+ icomp = 0;
+ String imname = null;
+ int i = 0;
+ for (DbSourceProxy sproxy : otherdb)
{
- dfetch.setText(mname + " to '" + dbname + "'");
- rfetch.add(dfetch);
- dfetch = new JMenu();
- mname = null;
- comp = 0;
+ String dbname = sproxy.getDbName();
+ String sname = dbname.length() > 5 ? dbname.substring(0,
+ 5) + "..." : dbname;
+ String msname = dbname.length() > 10 ? dbname.substring(
+ 0, 10) + "..." : dbname;
+ if (imname == null)
+ {
+ imname = "from '" + sname + "'";
+ }
+ fetchr = new JMenuItem(msname);
+ final DbSourceProxy[] dassrc =
+ { sproxy };
+ fetchr.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ new Thread(new Runnable()
+ {
+
+ public void run()
+ {
+ new jalview.ws.DBRefFetcher(alignPanel.av
+ .getSequenceSelection(),
+ alignPanel.alignFrame, dassrc)
+ .fetchDBRefs(false);
+ }
+ }).start();
+ }
+
+ });
+ fetchr.setToolTipText("<html>"
+ + JvSwingUtils.wrapTooltip("Retrieve from "
+ + dbname) + "</html>");
+ ifetch.add(fetchr);
+ ++i;
+ if (++icomp >= mcomp || i == (otherdb.size()))
+ {
+ ifetch.setText(imname + " to '" + sname + "'");
+ dfetch.add(ifetch);
+ ifetch = new JMenu();
+ imname = null;
+ icomp = 0;
+ comp++;
+ }
}
}
+ ++dbi;
+ if (comp >= mcomp || dbi >= (dbclasses.length))
+ {
+ dfetch.setText(mname + " to '" + dbclass + "'");
+ rfetch.add(dfetch);
+ dfetch = new JMenu();
+ mname = null;
+ comp = 0;
+ }
}
}
});
import jalview.datamodel.DBRefSource;\r
import jalview.datamodel.SequenceI;\r
import jalview.ws.dbsources.das.api.jalviewSourceI;\r
+import jalview.ws.dbsources.das.datamodel.DasSequenceSource;\r
import jalview.ws.seqfetcher.ASequenceFetcher;\r
import jalview.ws.seqfetcher.DbSourceProxy;\r
\r
}\r
\r
/**\r
- * return an ordered list of database sources suitable for using in a GUI\r
- * element\r
+ * return an ordered list of database sources where non-das database classes\r
+ * appear before das database classes\r
*/\r
public String[] getOrderedSupportedSources()\r
{\r
String[] srcs = this.getSupportedDb();\r
+ ArrayList<String> dassrc = new ArrayList<String>(), nondas = new ArrayList<String>();\r
+ for (int i = 0; i < srcs.length; i++)\r
+ {\r
+ boolean das = false,skip=false;\r
+ String nm;\r
+ for (DbSourceProxy dbs : getSourceProxy(srcs[i]))\r
+ {\r
+ // Skip the alignment databases for the moment - they're not useful for verifying a single sequence against its reference source\r
+ if (dbs.isA(DBRefSource.ALIGNMENTDB))\r
+ {\r
+ skip=true;\r
+ } else {\r
+ nm = dbs.getDbName();\r
+ if (getSourceProxy(srcs[i]) instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)\r
+ {\r
+ if (nm.startsWith("das:"))\r
+ {\r
+ nm = nm.substring(4);\r
+ das = true;\r
+ }\r
+ break;\r
+ }\r
+ }\r
+ }\r
+ if (skip)\r
+ {\r
+ continue;\r
+ }\r
+ if (das)\r
+ {\r
+ dassrc.add(srcs[i]);\r
+ }\r
+ else\r
+ {\r
+ nondas.add(srcs[i]);\r
+ }\r
+ }\r
+ String[] tosort = nondas.toArray(new String[0]), sorted = nondas\r
+ .toArray(new String[0]);\r
+ for (int j = 0, jSize = sorted.length; j < jSize; j++)\r
+ {\r
+ tosort[j] = tosort[j].toLowerCase();\r
+ }\r
+ jalview.util.QuickSort.sort(tosort, sorted);\r
+ // construct array with all sources listed\r
+\r
+ srcs = new String[sorted.length + dassrc.size()];\r
+ int i = 0;\r
+ for (int j = sorted.length - 1; j >= 0; j--, i++)\r
+ {\r
+ srcs[i] = sorted[j];\r
+ sorted[j] = null;\r
+ }\r
+\r
+ sorted = dassrc.toArray(new String[0]);\r
+ tosort = dassrc.toArray(new String[0]);\r
+ for (int j = 0, jSize = sorted.length; j < jSize; j++)\r
+ {\r
+ tosort[j] = tosort[j].toLowerCase();\r
+ }\r
+ jalview.util.QuickSort.sort(tosort, sorted);\r
+ for (int j = sorted.length - 1; j >= 0; j--, i++)\r
+ {\r
+ srcs[i] = sorted[j];\r
+ }\r
+ return srcs;\r
+ }\r
+\r
+ /**\r
+ * return plaintext databse list suitable for using in a GUI element\r
+ */\r
+ public String[] _getOrderedSupportedSources()\r
+ {\r
+ String[] srcs = this.getSupportedDb();\r
ArrayList dassrc = new ArrayList(), nondas = new ArrayList();\r
for (int i = 0; i < srcs.length; i++)\r
{\r
}\r
}\r
}\r
+\r
}\r
git://source.jalview.org / jalview.git / commitdiff