label.colourScheme_t-coffeescores = T-Coffee Scores
label.colourScheme_rnahelices = By RNA Helices
label.colourScheme_sequenceid = Sequence ID Colour
+label.colourScheme_gecos-flower = Gecos: flower
+label.colourScheme_gecos-blossom = Gecos: blossom
+label.colourScheme_gecos-sunset = Gecos: sunset
+label.colourScheme_gecos-ocean = Gecos: ocean
+label.colourScheme_igv = IGV Nucleotide
label.blc = BLC
label.fasta = Fasta
label.msf = MSF
label.colourScheme_t-coffeescores = Puntuación del T-Coffee
label.colourScheme_rnahelices = Por hélices de RNA
label.colourScheme_sequenceid = Color de ID de secuencia
+label.colourScheme_gecos-flower = Gecos: flower
+label.colourScheme_gecos-blossom = Gecos: blossom
+label.colourScheme_gecos-sunset = Gecos: sunset
+label.colourScheme_gecos-ocean = Gecos: ocean
+label.colourScheme_igv = IGV Nucleótido
label.blc = BLC
label.fasta = Fasta
label.msf = MSF
*/
package jalview.gui;
-import java.util.Locale;
-
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Component;
import java.util.HashMap;
import java.util.Hashtable;
import java.util.List;
+import java.util.Locale;
import java.util.Map;
import java.util.Vector;
import java.util.concurrent.CompletableFuture;
@Override
public void wrapMenuItem_actionPerformed(ActionEvent e)
{
- scaleAbove.setVisible(wrapMenuItem.isSelected());
- scaleLeft.setVisible(wrapMenuItem.isSelected());
- scaleRight.setVisible(wrapMenuItem.isSelected());
- viewport.setWrapAlignment(wrapMenuItem.isSelected());
+ wrapMenuItem_actionPerformed(e, wrapMenuItem.isSelected());
+ }
+
+ public void wrapMenuItem_actionPerformed(ActionEvent e, boolean select)
+ {
+ scaleAbove.setVisible(select);
+ scaleLeft.setVisible(select);
+ scaleRight.setVisible(select);
+ viewport.setWrapAlignment(select);
alignPanel.updateLayout();
+ wrapMenuItem.setSelected(select);
}
@Override
@Override
public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
{
- final boolean setVisible = annotationPanelMenuItem.isSelected();
+ annotationPanelMenuItem_actionPerformed(e,
+ annotationPanelMenuItem.isSelected());
+ }
+
+ public void annotationPanelMenuItem_actionPerformed(ActionEvent e,
+ boolean setVisible)
+ {
viewport.setShowAnnotation(setVisible);
this.showAllSeqAnnotations.setEnabled(setVisible);
this.hideAllSeqAnnotations.setEnabled(setVisible);
this.showAllAlAnnotations.setEnabled(setVisible);
this.hideAllAlAnnotations.setEnabled(setVisible);
+ annotationPanelMenuItem.setSelected(setVisible);
alignPanel.updateLayout();
}
*/
package jalview.gui;
-import jalview.bin.Cache;
+import java.awt.Toolkit;
+import java.awt.datatransfer.Clipboard;
+import java.awt.datatransfer.DataFlavor;
+import java.awt.datatransfer.StringSelection;
+import java.awt.datatransfer.Transferable;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseEvent;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.util.HashMap;
+import java.util.Map;
+
+import javax.swing.JMenuItem;
+import javax.swing.JPopupMenu;
+import javax.swing.SwingUtilities;
+
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.ComplexAlignFile;
import jalview.api.FeatureSettingsModelI;
import jalview.api.FeaturesDisplayedI;
import jalview.api.FeaturesSourceI;
+import jalview.bin.Cache;
import jalview.bin.Jalview;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.HiddenColumns;
import jalview.schemes.ColourSchemeI;
import jalview.util.MessageManager;
-import java.awt.Toolkit;
-import java.awt.datatransfer.Clipboard;
-import java.awt.datatransfer.DataFlavor;
-import java.awt.datatransfer.StringSelection;
-import java.awt.datatransfer.Transferable;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.MouseEvent;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.io.PrintWriter;
-
-import javax.swing.JMenuItem;
-import javax.swing.JPopupMenu;
-import javax.swing.SwingUtilities;
-
/**
* Cut'n'paste files into the desktop See JAL-1105
*
@Override
public void ok_actionPerformed(ActionEvent e)
{
+ ok_actionPerformed(e, new HashMap<String, String>());
+ }
+
+ public void ok_actionPerformed(ActionEvent e, Map<String, String> options)
+ {
String text = getText();
if (text.trim().length() < 1)
{
FormatAdapter fa = new FormatAdapter(alignpanel);
al = fa.readFile(getText(), DataSourceType.PASTE, format);
source = fa.getAlignFile();
-
} catch (IOException ex)
{
JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
if (al != null && al.hasValidSequence())
{
- String title = MessageManager
- .formatMessage("label.input_cut_paste_params", new String[]
- { format.getName() });
+ String title = options.containsKey("title") ? options.get("title")
+ : MessageManager.formatMessage("label.input_cut_paste_params",
+ new String[]
+ { format.getName() });
FeatureSettingsModelI proxyColourScheme = source
.getFeatureColourScheme();
af.getViewport().applyFeaturesStyle(proxyColourScheme);
}
af.currentFileFormat = format;
+ if (options.containsKey("wrap"))
+ {
+ af.wrapMenuItem_actionPerformed(e,
+ Boolean.parseBoolean(options.get("wrap")));
+ }
+ if (options.containsKey("showannotations"))
+ {
+ af.annotationPanelMenuItem_actionPerformed(e,
+ Boolean.parseBoolean(options.get("showannotations")));
+ }
+ if (options.containsKey("colourscheme"))
+ {
+ af.changeColour_actionPerformed(options.get("colourscheme"));
+ }
Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
af.setStatus(MessageManager
import java.io.IOException;
import java.io.PrintWriter;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Map.Entry;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
private final String description;
+ private String[] pathParameters = null;
+
+ private Map<String, String[]> queryParameters = null;
+
+ private Map<String, String> options = null;
+
+ private String id = null;
+
+ private String fromId = null;
+
public AbstractEndpoint(API api, String path, String name,
String parameters, String description)
{
* Shared methods below here
*/
+ protected String getId(HttpServletRequest request)
+ {
+ if (id != null)
+ return id;
+ id = getQueryParameter(request, "id");
+ return id;
+ }
+
+ protected String getFromId(HttpServletRequest request)
+ {
+ if (fromId != null)
+ return fromId;
+ fromId = getQueryParameter(request, "fromId");
+ return fromId;
+ }
+
+ protected Map<String, String[]> getQueryParameters(
+ HttpServletRequest request)
+ {
+ if (queryParameters != null)
+ return queryParameters;
+ queryParameters = request.getParameterMap();
+ return queryParameters;
+ }
+
+ protected String getQueryParameter(HttpServletRequest request,
+ String param)
+ {
+ String[] vals = getQueryParameters(request).get(param);
+ return (vals == null || vals.length < 1) ? null : vals[0];
+ }
+
protected String[] getEndpointPathParameters(HttpServletRequest request)
{
+ if (pathParameters != null)
+ return pathParameters;
String pathInfo = request.getPathInfo();
int slashpos = pathInfo.indexOf('/', 1);
- return slashpos < 1 ? null
- : pathInfo.substring(slashpos + 1).split("/");
+ if (slashpos < 1)
+ return null;
+
+ pathParameters = pathInfo.substring(slashpos + 1).split("/");
+ return pathParameters;
+ }
+
+ protected Map<String, String> getOptions(HttpServletRequest request)
+ {
+ if (this.options != null)
+ return this.options;
+ Map<String, String> opts = new HashMap<>();
+ for (Entry<String, String[]> e : getQueryParameters(null).entrySet())
+ {
+ if (e.getKey().startsWith("option:"))
+ {
+ for (int i = 0; i < e.getValue().length; i++)
+ {
+ opts.put(e.getKey().substring(7), e.getValue()[i]);
+ }
+ }
+ }
+
+ String[] params = getEndpointPathParameters(request);
+ if (params != null)
+ {
+ for (int i = 0; i < params.length; i++)
+ {
+ String param = params[i];
+ if (param.startsWith("option:"))
+ {
+ int ePos = param.indexOf("=");
+ if (ePos == -1)
+ {
+ opts.put(param.substring(7), null);
+ }
+ else
+ {
+ opts.put(param.substring(7, ePos), param.substring(ePos + 1));
+ }
+ }
+ }
+ }
+ this.options = opts;
+ return opts;
}
protected void returnError(HttpServletRequest request,
protected AlignFrame[] getAlignFrames(HttpServletRequest request,
String idParam, boolean all)
{
- String fromIdString = request.getParameter(idParam);
+ String fromIdString = this.getQueryParameter(request, idParam);
if (fromIdString != null)
{
String idParam)
{
AlignFrame[] afs = getAlignFrames(request, idParam, false);
- return (afs == null || afs.length < 1 || afs[0] == null) ? null
- : afs[0];
+ return (afs == null || afs.length < 1) ? null : afs[0];
}
protected boolean deleteFromCache()
HttpServletResponse response)
{
// should be overridden
- // must setId(request, extension)
- setId(request, null);
+ // MUST setId(request, extension)
+ this.setId(request, null);
+ // and do this
+ this.saveParameters(request);
+ }
+
+ protected void saveParameters(HttpServletRequest request)
+ {
+ this.getId(request);
+ this.getFromId(request);
+ this.getEndpointPathParameters(request);
+ this.getQueryParameters(request);
+ this.getOptions(request);
}
protected abstract void processAsync(HttpServletRequest request,
protected String setId(HttpServletRequest request, String extension)
{
- String idString = request.getParameter("id");
+ String idString = getId(request);
+ Console.debug("GOT ID '" + idString + "'");
if (idString == null)
{
setIdExtension(extension);
isPost = method.equalsIgnoreCase("post");
hasData = data != null;
+ this.saveParameters(request);
+
if (isPost)
{
access = "post";
try
{
body = RestHandler.getInstance().getRequestBody(request, response);
- Console.debug("BODY='" + body + "'");
} catch (IOException e)
{
returnError(request, response, "could not read POST body");
// use File -> Input Alignment -> from Textbox
CutAndPasteTransfer cap = new CutAndPasteTransfer();
cap.setText(content);
- cap.ok_actionPerformed(null);
+
+ Map<String, String> options = getOptions(request);
+
+ cap.ok_actionPerformed(null, options);
cap.cancel_actionPerformed(null);
}
else if (fileString != null)
import java.io.IOException;
import java.io.InputStreamReader;
import java.io.PrintWriter;
+import java.lang.reflect.InvocationTargetException;
import java.net.BindException;
import java.util.HashMap;
import java.util.Map;
private boolean init = false;
// map of method names and method handlers
- private Map<String, EndpointI> endpoints = null;
+ private Map<String, AbstractEndpoint> endpoints = null;
- protected Map<String, EndpointI> getEndpoints()
+ protected Map<String, AbstractEndpoint> getEndpoints()
{
return endpoints;
}
+ protected AbstractEndpoint getNewEndpoint(String name)
+ {
+ if (getEndpoints() == null)
+ {
+ return null;
+ }
+ try
+ {
+ return getEndpoints().get(name).getClass()
+ .getDeclaredConstructor(API.class).newInstance(this);
+ } catch (InstantiationException | IllegalAccessException
+ | IllegalArgumentException | InvocationTargetException
+ | NoSuchMethodException | SecurityException e)
+ {
+ Console.debug("Could not instantiate new endpoint '" + name + "'", e);
+ }
+ return null;
+ }
+
/**
* Singleton instance of this class
*/
// This "pointless" call to request.getInputStream() seems to preserve the
// InputStream for use later in getRequestBody.
request.getInputStream();
- if (endpoints == null)
+
+ String remoteAddr = request.getRemoteAddr();
+ if (!("127.0.0.1".equals(remoteAddr) || "localhost".equals(remoteAddr)))
+ {
+ returnError(request, response, "Not authorised: " + remoteAddr,
+ HttpServletResponse.SC_UNAUTHORIZED);
+ return;
+ }
+ if (getEndpoints() == null)
{
final String queryString = request.getQueryString();
final String reply = "REST not yet implemented; received "
+ request.getMethod() + ": " + request.getRequestURL()
+ (queryString == null ? "" : "?" + queryString);
- System.out.println(reply);
+ Console.error(reply);
response.setHeader("Cache-Control", "no-cache/no-store");
response.setHeader("Content-type", "text/plain");
String endpointName = getRequestedEndpointName(request);
- if (!endpoints.containsKey(endpointName)
- || endpoints.get(endpointName) == null)
+ if (!getEndpoints().containsKey(endpointName)
+ || getEndpoints().get(endpointName) == null)
{
response.setHeader("Cache-Control", "no-cache/no-store");
ContextHandler ch = HttpServer.getInstance().getContextHandler(this);
String base = HttpServer.getInstance().getUri().toString();
String contextPath = ch == null ? "" : ch.getContextPath();
- for (String key : endpoints.keySet())
+ for (String key : getEndpoints().keySet())
{
writer.write(base + contextPath + "/" + key + "\n");
}
response.setHeader("Cache-Control", "no-cache/no-store");
response.setHeader("Content-type", "text/plain");
- EndpointI ep = endpoints.get(endpointName);
+ EndpointI ep = getNewEndpoint(endpointName);
ep.processEndpoint(request, response);
return;
// e.g. registerHandler and addEndpoints
}
- protected boolean addEndpoint(EndpointI ep)
+ protected void addEndpoint(AbstractEndpoint ep)
{
- if (endpoints == null)
+ if (getEndpoints() == null)
{
endpoints = new HashMap<>();
}
- AbstractEndpoint e = (AbstractEndpoint) ep;
endpoints.put(ep.getPath(), ep);
- return true;
+ Console.debug("REST API, added endpoint '" + ep.getPath() + "'");
}
protected String getRequestedEndpointName(HttpServletRequest request)
: pathInfo.substring(1);
}
- protected String[] getEndpointPathParameters(HttpServletRequest request)
+ protected void returnError(HttpServletRequest request,
+ HttpServletResponse response, String message)
{
- String pathInfo = request.getPathInfo();
- int slashpos = pathInfo.indexOf('/', 1);
- return slashpos < 1 ? null
- : pathInfo.substring(slashpos + 1).split("/");
+ returnError(request, response, message,
+ HttpServletResponse.SC_INTERNAL_SERVER_ERROR);
}
protected void returnError(HttpServletRequest request,
- HttpServletResponse response, String message)
+ HttpServletResponse response, String message, int statusCode)
{
- response.setStatus(HttpServletResponse.SC_INTERNAL_SERVER_ERROR);
+ response.setStatus(statusCode);
String endpointName = getRequestedEndpointName(request);
Console.error(getName() + " error: endpoint " + endpointName
+ " failed: '" + message + "'");
StringBuilder sb = new StringBuilder();
BufferedReader reader = null;
Console.debug("REQUEST=" + request.toString());
- Console.debug("REQUEST.Content-Lenggth=" + request.getContentLength());
+ Console.debug("REQUEST.Content-Length=" + request.getContentLength());
try
{
reader = request.getReader();
} catch (IllegalStateException e)
{
ServletInputStream is = request.getInputStream();
- Console.debug("INPUTSTREAM "
- + (is.isFinished() ? "FINISHED" : "NOT FINISHED"));
reader = new BufferedReader(new InputStreamReader(is));
Console.debug("Using getInputStream()");
}
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview 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 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.schemes;
+
+import jalview.api.AlignViewportI;
+import jalview.datamodel.AnnotatedCollectionI;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class IGVColourScheme extends ResidueColourScheme
+{
+ /**
+ * Creates a new NucleotideColourScheme object.
+ */
+ public IGVColourScheme()
+ {
+ super(ResidueProperties.nucleotideIndex, ResidueProperties.igv);
+ }
+
+ @Override
+ public boolean isNucleotideSpecific()
+ {
+ return true;
+ }
+
+ @Override
+ public String getSchemeName()
+ {
+ return JalviewColourScheme.IGV.toString();
+ }
+
+ /**
+ * Returns a new instance of this colour scheme with which the given data may
+ * be coloured
+ */
+ @Override
+ public ColourSchemeI getInstance(AlignViewportI view,
+ AnnotatedCollectionI coll)
+ {
+ return new IGVColourScheme();
+ }
+}
PID("% Identity", PIDColourScheme.class),
Zappo("Zappo", ZappoColourScheme.class),
Taylor("Taylor", TaylorColourScheme.class),
- Flower("gecos:flower", FlowerColourScheme.class),
- Blossom("gecos:blossom", BlossomColourScheme.class),
- Sunset("gecos:sunset", SunsetColourScheme.class),
- Ocean("gecos:ocean", OceanColourScheme.class),
+ Flower("gecos-flower", FlowerColourScheme.class),
+ Blossom("gecos-blossom", BlossomColourScheme.class),
+ Sunset("gecos-sunset", SunsetColourScheme.class),
+ Ocean("gecos-ocean", OceanColourScheme.class),
Hydrophobic("Hydrophobic", HydrophobicColourScheme.class),
Helix("Helix Propensity", HelixColourScheme.class),
Strand("Strand Propensity", StrandColourScheme.class),
Turn("Turn Propensity", TurnColourScheme.class),
Buried("Buried Index", BuriedColourScheme.class),
Nucleotide("Nucleotide", NucleotideColourScheme.class),
+ IGV("IGV", IGVColourScheme.class),
PurinePyrimidine("Purine/Pyrimidine", PurinePyrimidineColourScheme.class),
RNAHelices("RNA Helices", RNAHelicesColour.class),
TCoffee("T-Coffee Scores", TCoffeeColourScheme.class),
Color.white, // Gap
};
+ public static final Color[] igv = {
+ new Color(0, 150, 0), // A
+ Color.blue, // C
+ new Color(209, 113, 5), // G
+ Color.red, // T
+ Color.red, // U
+ Color.white, // I (inosine)
+ Color.white, // X (xanthine)
+ Color.white, // R
+ Color.white, // Y
+ Color.white, // N
+ Color.white, // Gap
+ };
+
// Added for PurinePyrimidineColourScheme
public static final Color[] purinepyrimidine = { new Color(255, 131, 250), // A,
// G,
git://source.jalview.org / jalview.git / commitdiff