* @param seqRef
* @param startRes
* @param alreadyMapped
+ * - annotation are at aligned columns
*/
public void createSequenceMapping(SequenceI seqRef, int startRes,
boolean alreadyMapped)
* already
*/
public void remap(SequenceI newref, HashMap<Integer, int[]> mapping,
- int from, int to,
- int idxoffset)
+ int from, int to, int idxoffset)
{
if (mapping != null)
{
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
- /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
- */
package jalview.gui;
import jalview.analysis.AlignmentUtils;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SearchResults;
+ import jalview.datamodel.SearchResultsI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
setFont(new Font(fontName, style, Integer.parseInt(fontSize)), true);
- alignment
- .setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
-
+ if (Cache.getDefault("NORMALISE_GAPS", true))
+ {
+ alignment.setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(
+ 0));
+ }
// We must set conservation and consensus before setting colour,
// as Blosum and Clustal require this to be done
if (hconsensus == null && !isDataset)
List<SequenceI> choosenSeqs = new ArrayList<SequenceI>();
for (SequenceI sq : alignment.getSequences())
{
- Vector<PDBEntry> pdbRefEntries = sq.getDatasetSequence().getAllPDBEntries();
+ Vector<PDBEntry> pdbRefEntries = sq.getDatasetSequence()
+ .getAllPDBEntries();
if (pdbRefEntries == null)
{
continue;
}
}
}
- seqvectors.add(choosenSeqs.toArray(new SequenceI[choosenSeqs.size()]));
+ seqvectors
+ .add(choosenSeqs.toArray(new SequenceI[choosenSeqs.size()]));
}
return seqvectors.toArray(new SequenceI[seqvectors.size()][]);
}
MessageManager.getString("label.new_window"), };
final String question = JvSwingUtils.wrapTooltip(true,
MessageManager.getString("label.open_split_window?"));
- int response = JOptionPane.showOptionDialog(Desktop.desktop, question,
+ int response = JvOptionPane.showOptionDialog(Desktop.desktop, question,
MessageManager.getString("label.open_split_window"),
- JOptionPane.DEFAULT_OPTION, JOptionPane.PLAIN_MESSAGE, null,
+ JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
options, options[0]);
if (response != 1 && response != 2)
// TODO if we want this (e.g. to enable reload of the alignment from file),
// we will need to add parameters to the stack.
- // if (!protocol.equals(AppletFormatAdapter.PASTE))
+ // if (!protocol.equals(DataSourceType.PASTE))
// {
// alignFrame.setFileName(file, format);
// }
* there is no complement, or it is not following highlights, or no mapping
* is found, the result will be empty.
*/
- SearchResults sr = new SearchResults();
+ SearchResultsI sr = new SearchResults();
int verticalOffset = findComplementScrollTarget(sr);
if (!sr.isEmpty())
{
*/
public static final boolean isGap(char c)
{
- return (c == GAP_DASH || c == GAP_DOT || c == GAP_SPACE) ? true : false;
+ return (c == GAP_DASH || c == GAP_DOT || c == GAP_SPACE);
}
/**
.size()]);
return isNucleotide(oneDArray);
}
+
+ /**
+ * Compares two residues either case sensitively or case insensitively
+ * depending on the caseSensitive flag
+ *
+ * @param c1
+ * first char
+ * @param c2
+ * second char to compare with
+ * @param caseSensitive
+ * if true comparison will be case sensitive otherwise its not
+ * @return
+ */
+ public static boolean isSameResidue(char c1, char c2,
+ boolean caseSensitive)
+ {
+ if (caseSensitive)
+ {
+ return (c1 == c2);
+ }
+ else
+ {
+ return Character.toUpperCase(c1) == Character.toUpperCase(c2);
+ }
+ }
}
- /*******************************************************************************
+ /*
* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* You should have received a copy of the GNU General Public License
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
- ******************************************************************************/
+ */
package jalview.util;
+import java.io.BufferedInputStream;
+import java.io.File;
+import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.net.URL;
return false;
}
+ /**
+ * download from given URL and return a pointer to temporary file
+ */
+ public static File fetchURLToTemp(String url) throws OutOfMemoryError,
+ IOException
+ {
+ long time = System.currentTimeMillis();
+ URL rcall = new URL(url);
+
+ InputStream is = new BufferedInputStream(rcall.openStream());
+ File outFile = null;
+ try
+ {
+ outFile = File.createTempFile("jalview", ".xml");
+ outFile.deleteOnExit();
+ if (outFile.length() == 0)
+ {
+ outFile.delete();
+ return null;
+ }
+ } catch (Exception ex)
+ {
+ }
+
+ if (outFile != null)
+ {
+ FileOutputStream fio = new FileOutputStream(outFile);
+ byte[] bb = new byte[32 * 1024];
+ int l;
+ while ((l = is.read(bb)) > 0)
+ {
+ fio.write(bb, 0, l);
+ }
+ fio.close();
+ is.close();
+ return outFile;
+ }
+ else
+ {
+ return null;
+ }
+ }
}
import jalview.gui.AlignViewport;
import jalview.gui.AlignmentPanel;
import jalview.gui.Desktop;
+ import jalview.gui.JvOptionPane;
import jalview.gui.WebserviceInfo;
-import jalview.io.packed.DataProvider.JvDataType;
import jalview.util.MessageManager;
import jalview.ws.WSClient;
import jalview.ws.WSClientI;
import jalview.ws.WSMenuEntryProviderI;
+import jalview.ws.rest.clientdefs.ShmrRestClient;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
-import java.util.Hashtable;
import java.util.Vector;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
- import javax.swing.JOptionPane;
import javax.swing.event.MenuEvent;
import javax.swing.event.MenuListener;
else
{
// TODO: try to tell the user why the job couldn't be started.
- JOptionPane
+ JvOptionPane
.showMessageDialog(
Desktop.desktop,
(jobsthread.hasWarnings() ? jobsthread.getWarnings()
.getString("label.job_couldnt_be_started_check_input")),
MessageManager
.getString("label.unable_start_web_service_analysis"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
}
}
- public static RestClient makeShmmrRestClient()
- {
- String action = "Analysis", description = "Sequence Harmony and Multi-Relief (Brandt et al. 2010)", name = MessageManager
- .getString("label.multiharmony");
- Hashtable<String, InputType> iparams = new Hashtable<String, InputType>();
- jalview.ws.rest.params.JobConstant toolp;
- // toolp = new jalview.ws.rest.JobConstant("tool","jalview");
- // iparams.put(toolp.token, toolp);
- // toolp = new jalview.ws.rest.params.JobConstant("mbjob[method]","shmr");
- // iparams.put(toolp.token, toolp);
- // toolp = new
- // jalview.ws.rest.params.JobConstant("mbjob[description]","step 1");
- // iparams.put(toolp.token, toolp);
- // toolp = new jalview.ws.rest.params.JobConstant("start_search","1");
- // iparams.put(toolp.token, toolp);
- // toolp = new jalview.ws.rest.params.JobConstant("blast","0");
- // iparams.put(toolp.token, toolp);
-
- jalview.ws.rest.params.Alignment aliinput = new jalview.ws.rest.params.Alignment();
- // SHMR server has a 65K limit for content pasted into the 'ali' parameter,
- // so we always upload our files.
- aliinput.token = "ali_file";
- aliinput.writeAsFile = true;
- iparams.put(aliinput.token, aliinput);
- jalview.ws.rest.params.SeqGroupIndexVector sgroups = new jalview.ws.rest.params.SeqGroupIndexVector();
- sgroups.setMinsize(2);
- sgroups.min = 2;// need at least two group defined to make a partition
- iparams.put("groups", sgroups);
- sgroups.token = "groups";
- sgroups.sep = " ";
- RestServiceDescription shmrService = new RestServiceDescription(
- action,
- description,
- name,
- "http://zeus.few.vu.nl/programs/shmrwww/index.php?tool=jalview",// ?tool=jalview&mbjob[method]=shmr&mbjob[description]=step1",
- "?tool=jalview", iparams, true, false, '-');
- // a priori knowledge of the data returned from the service
- shmrService.addResultDatatype(JvDataType.ANNOTATION);
- return new RestClient(shmrService);
- }
-
public AlignmentPanel recoverAlignPanelForView()
{
AlignmentPanel[] aps = Desktop
for (RestServiceDescription descr : RestServiceDescription
.parseDescriptions(jalview.bin.Cache.getDefault(
RSBS_SERVICES,
- makeShmmrRestClient().service.toString())))
+ ShmrRestClient.makeShmmrRestClient().service.toString())))
{
services.add(descr.toString());
}
import static org.testng.AssertJUnit.assertTrue;
import jalview.gui.AlignFrame;
+ import jalview.gui.JvOptionPane;
+import jalview.ws.rest.clientdefs.ShmrRestClient;
import java.util.Map;
+ import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
/**
public class ShmmrRSBSService
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = { "Functional" })
public void testShmmrService()
{
assertTrue(
"Test Rsd Exchange using using default Shmmr service failed.",
testRsdExchange("Test using default Shmmr service",
- RestClient.makeShmmrRestClient().service));
+ ShmrRestClient.makeShmmrRestClient().service));
}
@Test(groups = { "Functional" })
public void testShmmrServiceDataprep() throws Exception
{
- RestClient _rc = RestClient.makeShmmrRestClient();
+ RestClient _rc = ShmrRestClient.makeShmmrRestClient();
assertNotNull(_rc);
AlignFrame alf = new jalview.io.FileLoader(false)
.LoadFileWaitTillLoaded("examples/testdata/smad.fa",
- jalview.io.FormatAdapter.FILE);
+ jalview.io.DataSourceType.FILE);
assertNotNull("Couldn't find test data.", alf);
alf.loadJalviewDataFile("examples/testdata/smad_groups.jva",
- jalview.io.FormatAdapter.FILE, null, null);
+ jalview.io.DataSourceType.FILE, null, null);
assertTrue(
"Couldn't load the test data's annotation file (should be 5 groups but found "
+ alf.getViewport().getAlignment().getGroups().size()
git://source.jalview.org / jalview.git / commitdiff