Changeset 3128

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Timestamp:
02/27/10 20:18:26 (5 months ago)
Author:
martijn
Message:

Updated to new org.bridgedb.rdb.construct pacakge

Location:
trunk
Files:
1 added
12 modified

Legend:

Unmodified
Added
Removed

  • trunk/build.xml

    r3127 r3128  
    4848          <path refid="core.libs"/> 
    4949          <fileset dir="lib"> 
     50                <include name="org.bridgedb.rdb.construct.jar"/> 
    5051            <include name="derby.jar"/> 
    5152                <include name="forms-1.2.0.jar"/> 
    … …  
    99100                <pathelement location="${build.swing.dir}"/> 
    100101                <fileset dir="lib"> 
     102                        <include name="org.bridgedb.rdb.construct.jar"/> 
    101103                        <include name="BrowserLauncher.jar"/> 
    102104                        <include name="commons-math-2.0.jar"/> 

  • trunk/plugins/GexPlugin/src/org/pathvisio/plugins/gex/GexImportWizard.java

    r3125 r3128  
    5959 
    6060import org.bridgedb.IDMapperException; 
    61 import org.bridgedb.rdb.DBConnector; 
     61import org.bridgedb.rdb.construct.DBConnector; 
    6262import org.jdesktop.swingworker.SwingWorker; 
    6363import org.pathvisio.data.DBConnectorSwing; 

  • trunk/plugins/GexPlugin/src/org/pathvisio/plugins/gex/GexPlugin.java

    r2979 r3128  
    2222import javax.swing.JOptionPane; 
    2323 
    24 import org.bridgedb.rdb.DBConnector; 
     24import org.bridgedb.rdb.construct.DBConnector; 
    2525import org.pathvisio.data.DBConnectorSwing; 
    2626import org.pathvisio.debug.Logger; 

  • trunk/plugins/GexPlugin/test/org/pathvisio/plugins/gex/Test.java

    r2979 r3128  
    2323import java.util.List; 
    2424 
     25import junit.framework.TestCase; 
     26 
     27import org.bridgedb.BridgeDb; 
     28import org.bridgedb.IDMapper; 
    2529import org.bridgedb.IDMapperException; 
    26 import org.bridgedb.DataSource; 
    2730import org.bridgedb.Xref; 
    2831import org.bridgedb.bio.BioDataSource; 
    29 import org.bridgedb.rdb.DBConnector; 
    30 import org.bridgedb.rdb.DataDerby; 
    31 import org.bridgedb.rdb.DataDerbyDirectory; 
    32 import org.bridgedb.rdb.IDMapperRdb; 
    33 import org.bridgedb.rdb.SimpleGdb; 
    34 import org.bridgedb.rdb.SimpleGdbFactory; 
     32import org.bridgedb.rdb.construct.DBConnector; 
     33import org.bridgedb.rdb.construct.DataDerby; 
     34import org.bridgedb.rdb.construct.DataDerbyDirectory; 
    3535import org.pathvisio.gex.CachedData; 
    3636import org.pathvisio.gex.GexManager; 
    … …  
    3838import org.pathvisio.gex.Sample; 
    3939import org.pathvisio.gex.SimpleGex; 
    40 import org.pathvisio.plugins.gex.GexTxtImporter; 
    41 import org.pathvisio.plugins.gex.ImportInformation; 
    4240import org.pathvisio.preferences.PreferenceManager; 
    43  
    44 import junit.framework.TestCase; 
    4541 
    4642public class Test extends TestCase 
    … …  
    5652        GexManager gexManager = null; 
    5753 
    58         public void setUp() 
     54        public void setUp() throws ClassNotFoundException 
    5955        { 
    6056                gexManager = GexManager.getCurrent(); 
     57                Class.forName ("org.bridgedb.rdb.IDMapperRdb"); 
    6158        } 
    6259 
    … …  
    8885                String dbFileName = System.getProperty("java.io.tmpdir") + File.separator + "tempgex2"; 
    8986                info.setGexName(dbFileName); 
    90                 SimpleGdb gdb = SimpleGdbFactory.createInstance(GDB_HUMAN, new DataDerby(), 0); 
     87                IDMapper gdb = BridgeDb.connect("idmapper-pgdb:" + GDB_HUMAN); 
    9188                GexTxtImporter.importFromTxt(info, null, gdb, gexManager); 
    9289 
    … …  
    134131                info2.setGexName(dbFileName); 
    135132 
    136                 IDMapperRdb gdb = SimpleGdbFactory.createInstance (GDB_RAT, new DataDerby(), 0); 
     133                IDMapper gdb = BridgeDb.connect("idmapper-pgdb:" + GDB_HUMAN); 
    137134                GexTxtImporter.importFromTxt(info2, null, gdb, gexManager); 
    138135 
    … …  
    158155                info.setSyscodeFixed(true); 
    159156                info.setDataSource(BioDataSource.AFFY); 
    160                 SimpleGdb gdb = SimpleGdbFactory.createInstance (GDB_RAT, new DataDerby(), 0); 
     157                IDMapper gdb = BridgeDb.connect("idmapper-pgdb:" + GDB_RAT); 
    161158                GexTxtImporter.importFromTxt(info, null, gdb, gexManager); 
    162159 
    … …  
    185182                info.setGexName(dbFileName); 
    186183 
    187                 SimpleGdb gdb = SimpleGdbFactory.createInstance(GDB_HUMAN, new DataDerby(), 0); 
     184                IDMapper gdb = BridgeDb.connect("idmapper-pgdb:" + GDB_HUMAN); 
    188185                GexTxtImporter.importFromTxt(info, null, gdb, gexManager); 
    189186 
    … …  
    211208                info.setGexName(dbFileName); 
    212209 
    213                 SimpleGdb gdb = SimpleGdbFactory.createInstance(GDB_HUMAN, new DataDerby(), 0); 
     210                IDMapper gdb = BridgeDb.connect("idmapper-pgdb:" + GDB_HUMAN); 
    214211                GexTxtImporter.importFromTxt(info, null, gdb, gexManager); 
    215212 
    … …  
    239236                info.setGexName(dbFileName); 
    240237 
    241                 SimpleGdb gdb = SimpleGdbFactory.createInstance(GDB_HUMAN, new DataDerby(), 0); 
     238                IDMapper gdb = BridgeDb.connect("idmapper-pgdb:" + GDB_HUMAN); 
    242239                GexTxtImporter.importFromTxt(info, null, gdb, gexManager); 
    243240 

  • trunk/plugins/zscore/org/pathvisio/plugins/statistics/IsDataInPathways.java

    r2979 r3128  
    2828import java.util.regex.Pattern; 
    2929 
     30import org.bridgedb.AttributeMapper; 
     31import org.bridgedb.BridgeDb; 
     32import org.bridgedb.IDMapper; 
    3033import org.bridgedb.IDMapperException; 
    3134import org.bridgedb.Xref; 
    32 import org.bridgedb.rdb.DataDerby; 
    3335import org.bridgedb.rdb.SimpleGdb; 
    3436import org.bridgedb.rdb.SimpleGdbFactory; 
     37import org.bridgedb.rdb.construct.DataDerby; 
    3538import org.pathvisio.data.XrefWithSymbol; 
    3639import org.pathvisio.debug.Logger; 
    … …  
    9093                Map<Xref, List<String>> counts = new HashMap<Xref, List<String>>(); 
    9194 
    92                 SimpleGdb gdb = SimpleGdbFactory.createInstance("" + fGdb, new DataDerby(), 0); 
     95                IDMapper gdb = BridgeDb.connect("idmapper-pgdb:" + fGdb); 
    9396 
    9497                for (int i = 0; i < gex.getNrRow(); ++i) 
    … …  
    123126                        ReporterData data = gex.getRow(i); 
    124127                        Xref ref = data.getXref(); 
    125                         String bpText = Utils.oneOf (gdb.getAttributes(ref, "Backpage")); 
     128                        String bpText = Utils.oneOf (((AttributeMapper)gdb).getAttributes(ref, "Backpage")); 
    126129                        String desc = ""; 
    127130                        if (bpText != null) 

  • trunk/src/swing/org/pathvisio/data/DBConnDerby.java

    r2979 r3128  
    2121import javax.swing.JFileChooser; 
    2222 
    23 import org.bridgedb.rdb.DataDerby; 
     23import org.bridgedb.rdb.construct.DataDerby; 
    2424import org.pathvisio.preferences.GlobalPreference; 
    2525import org.pathvisio.preferences.PreferenceManager; 

  • trunk/src/swing/org/pathvisio/gex/GexManager.java

    r2979 r3128  
    2222 
    2323import org.bridgedb.IDMapperException; 
    24 import org.bridgedb.rdb.DBConnector; 
     24import org.bridgedb.rdb.construct.DBConnector; 
    2525import org.pathvisio.debug.Logger; 
    2626import org.pathvisio.preferences.GlobalPreference; 

  • trunk/src/swing/org/pathvisio/gex/SimpleGex.java

    r3122 r3128  
    3434import org.bridgedb.IDMapperException; 
    3535import org.bridgedb.Xref; 
    36 import org.bridgedb.rdb.DBConnector; 
     36import org.bridgedb.rdb.construct.DBConnector; 
    3737import org.pathvisio.debug.Logger; 
    3838 

  • trunk/tools/gexview/org/pathvisio/plugins/gexview/ApplicationWindow.java

    r2987 r3128  
    3030 
    3131import org.bridgedb.IDMapperException; 
    32 import org.bridgedb.rdb.DataDerby; 
     32import org.bridgedb.rdb.construct.DataDerby; 
    3333import org.pathvisio.Revision; 
    3434import org.pathvisio.gex.SimpleGex;