for (int i = 0; i < seqs.length; i++)
{
SequenceFeature[] sf = seqs[i].getSequenceFeatures();
- if (sf == null && seqs[i].getDatasetSequence() != null)
- {
- sf = seqs[i].getDatasetSequence().getSequenceFeatures();
- }
if (sf == null)
{
sf = new SequenceFeature[0];
|| !(aaRes == translated.charAt(0)))
{
// debug
- System.out.println(("Mismatch at " + i + "/" + aaResidue + ": "
- + codon + "(" + translated + ") != " + aaRes));
+ // System.out.println(("Mismatch at " + i + "/" + aaResidue + ": "
+ // + codon + "(" + translated + ") != " + aaRes));
return false;
}
}
MapList map, Map<String, Object> featureTypes,
Map<String, Boolean> featureGroups)
{
- SequenceFeature[] sfs = (dna.getDatasetSequence() != null ? dna
- .getDatasetSequence() : dna).getSequenceFeatures();
+ SequenceFeature[] sfs = dna.getSequenceFeatures();
Boolean fgstate;
DBRefEntry[] dnarefs = DBRefUtils.selectRefs(dna.getDBRef(),
DBRefSource.DNACODINGDBS);
return file;
}
- // public LoadingThread(String _file, JalviewLite _applet)
- // {
- // this._file = _file;
- // applet = _applet;
- // }
-
public LoadingThread(String file, String file2, JalviewLite _applet)
{
this._file = file;
int tfeat = 0;
if (sq != null)
{
- SequenceI dsq = sq.getDatasetSequence();
- while (dsq.getDatasetSequence() != null)
- {
- dsq = dsq.getDatasetSequence();
- }
- ;
- SequenceFeature[] sf = dsq.getSequenceFeatures();
+ SequenceFeature[] sf = sq.getSequenceFeatures();
if (sf != null)
{
int ist = sq.findIndex(sq.getStart());
import jalview.util.MessageManager;
import jalview.ws.HttpClientUtils;
+import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStreamReader;
import java.io.Reader;
// return processJsonResponseFor(HttpClientUtils.doHttpUrlPost(twoDtoolsURL,
// vals));
ArrayList<Reader> readers = new ArrayList<Reader>();
- readers.add(HttpClientUtils.doHttpUrlPost(twoDtoolsURL, vals, 0, 0));
+ final BufferedReader postResponse = HttpClientUtils.doHttpUrlPost(twoDtoolsURL, vals, 0, 0);
+ readers.add(postResponse);
return readers.iterator();
}
*/
package jalview.ext.rbvi.chimera;
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.TreeMap;
+
import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
import jalview.datamodel.AlignmentI;
import jalview.util.ColorUtils;
import jalview.util.Comparison;
-import java.awt.Color;
-import java.util.ArrayList;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.TreeMap;
-
/**
* Routines for generating Chimera commands for Jalview/Chimera binding
*
final Map<String, List<int[]>> modelData = colourData.get(model);
for (String chain : modelData.keySet())
{
+ boolean hasChain = !"".equals(chain.trim());
for (int[] range : modelData.get(chain))
{
if (!firstPositionForModel)
{
sb.append(range[0]).append("-").append(range[1]);
}
- sb.append(".").append(chain);
+ if (hasChain)
+ {
+ sb.append(".").append(chain);
+ }
firstPositionForModel = false;
}
}
sy = s * av.getCharHeight() + scaleHeight;
SequenceI seq = av.getAlignment().getSequenceAt(s);
- SequenceFeature[] features = seq.getDatasetSequence()
- .getSequenceFeatures();
+ SequenceFeature[] features = seq.getSequenceFeatures();
SequenceGroup[] groups = av.getAlignment().findAllGroups(seq);
for (res = 0; res < alwidth; res++)
{
public class AnnotationLabels extends JPanel implements MouseListener,
MouseMotionListener, ActionListener
{
+ private static final Pattern LEFT_ANGLE_BRACKET_PATTERN = Pattern.compile("<");
+
String TOGGLE_LABELSCALE = MessageManager.getString("label.scale_label_to_column");
String ADDNEW = MessageManager.getString("label.add_new_row");
|| (desc.substring(0, 6).toLowerCase().indexOf("<html>") < 0))
{
// clean the description ready for embedding in html
- desc = new StringBuffer(Pattern.compile("<").matcher(desc)
+ desc = new StringBuffer(LEFT_ANGLE_BRACKET_PATTERN.matcher(desc)
.replaceAll("<"));
desc.insert(0, "<html>");
}
String group;
for (int i = 0; i < af.getViewport().getAlignment().getHeight(); i++)
{
- if (af.getViewport().getAlignment().getSequenceAt(i)
- .getDatasetSequence().getSequenceFeatures() == null)
+ tmpfeatures = af.getViewport().getAlignment().getSequenceAt(i)
+ .getSequenceFeatures();
+ if (tmpfeatures == null)
{
continue;
}
- tmpfeatures = af.getViewport().getAlignment().getSequenceAt(i)
- .getDatasetSequence().getSequenceFeatures();
-
int index = 0;
while (index < tmpfeatures.length)
{
{
tmpfeatures = af.getViewport().getAlignment().getSequenceAt(i)
- .getDatasetSequence().getSequenceFeatures();
+ .getSequenceFeatures();
if (tmpfeatures == null)
{
continue;
// build a new links menu based on the current links + any non-positional
// features
Vector nlinks = new Vector(Preferences.sequenceURLLinks);
- SequenceFeature sf[] = sq == null ? null : sq.getDatasetSequence()
- .getSequenceFeatures();
+ SequenceFeature sf[] = sq == null ? null : sq.getSequenceFeatures();
for (int sl = 0; sf != null && sl < sf.length; sl++)
{
if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0)
}
}
- if (jdatasq.getSequenceFeatures() != null)
+ if (jds.getSequenceFeatures() != null)
{
- jalview.datamodel.SequenceFeature[] sf = jdatasq
+ jalview.datamodel.SequenceFeature[] sf = jds
.getSequenceFeatures();
int index = 0;
while (index < sf.length)
*/
package jalview.gui;
+import java.awt.Color;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.Hashtable;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.TreeMap;
+import java.util.Vector;
+
+import javax.swing.ButtonGroup;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JColorChooser;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JPopupMenu;
+import javax.swing.JRadioButtonMenuItem;
+
import jalview.analysis.AAFrequency;
import jalview.analysis.AlignmentAnnotationUtils;
import jalview.analysis.Conservation;
import jalview.util.MessageManager;
import jalview.util.UrlLink;
-import java.awt.Color;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.Hashtable;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.TreeMap;
-import java.util.Vector;
-
-import javax.swing.ButtonGroup;
-import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JColorChooser;
-import javax.swing.JMenu;
-import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
-import javax.swing.JPopupMenu;
-import javax.swing.JRadioButtonMenuItem;
-
/**
* DOCUMENT ME!
*
}
cap.setText("<html>" + contents.toString() + "</html>");
- Desktop.instance.addInternalFrame(cap, MessageManager.formatMessage(
+ Desktop.addInternalFrame(cap, MessageManager.formatMessage(
"label.sequence_details_for",
(sequences.length == 1 ? new Object[]
{ sequences[0].getDisplayId(true) } : new Object[]
{
for (SequenceI sq : alsqs)
{
- if ((sfs = (sq).getDatasetSequence().getSequenceFeatures()) != null)
+ if ((sfs = sq.getSequenceFeatures()) != null)
{
if (sfs.length > 0)
{
seqPojo.setName(name.toString());
seqPojo.setSeq(seq.getSequenceAsString());
- SequenceFeature[] seqFeatures = seq.getDatasetSequence()
- .getSequenceFeatures();
+ SequenceFeature[] seqFeatures = seq.getSequenceFeatures();
if (seqFeatures != null)
{
ArrayList<BioJsFeaturePojo> bjsSeqFeatures = new ArrayList<BioJsFeaturePojo>();
*/
package jalview.io;
+
import java.util.ArrayList;
import java.util.Hashtable;
import java.util.List;
}
// ADD NON POSITIONAL SEQUENCE INFO
- SequenceFeature[] features = ds.getSequenceFeatures();
+ SequenceFeature[] features = sequence.getSequenceFeatures();
if (showNpFeats && features != null)
{
for (int i = 0; i < features.length; i++)
{
feature = ds.getSequenceFeatures()[0].type;
}
+ // ?bug - feature may still have previous loop value
String key = type2id(feature);
if (key == null)
boolean offscreenRender = false;
- /**
- * DOCUMENT ME!
- *
- * @param g
- * DOCUMENT ME!
- * @param seq
- * DOCUMENT ME!
- * @param sg
- * DOCUMENT ME!
- * @param start
- * DOCUMENT ME!
- * @param end
- * DOCUMENT ME!
- * @param x1
- * DOCUMENT ME!
- * @param y1
- * DOCUMENT ME!
- * @param width
- * DOCUMENT ME!
- * @param height
- * DOCUMENT ME!
- */
protected SequenceI lastSeq;
char s;
charOffset = (av_charWidth - fm.charWidth(s)) / 2;
g.drawString(String.valueOf(s), charOffset
+ (av_charWidth * (i - start)), pady);
-
}
}
}
charOffset = (av_charWidth - fm.charWidth(s)) / 2;
g.drawString(String.valueOf(s), charOffset
+ (av_charWidth * (i - start)), pady);
-
}
}
}
return initialCol;
}
- SequenceFeature[] sf = seq.getSequenceFeatures();
+ SequenceFeature[] sequenceFeatures = seq.getSequenceFeatures();
if (seq != lastSeq)
{
lastSeq = seq;
- sequenceFeatures = sf;
- if (sequenceFeatures != null)
+ lastSequenceFeatures = sequenceFeatures;
+ if (lastSequenceFeatures != null)
{
- sfSize = sequenceFeatures.length;
+ sfSize = lastSequenceFeatures.length;
}
}
else
{
- if (sequenceFeatures != sf)
+ if (lastSequenceFeatures != sequenceFeatures)
{
- sequenceFeatures = sf;
- if (sequenceFeatures != null)
+ lastSequenceFeatures = sequenceFeatures;
+ if (lastSequenceFeatures != null)
{
- sfSize = sequenceFeatures.length;
+ sfSize = lastSequenceFeatures.length;
}
}
}
- if (sequenceFeatures == null || sfSize == 0)
+ if (lastSequenceFeatures == null || sfSize == 0)
{
return initialCol;
}
}
- private volatile SequenceFeature[] sequenceFeatures;
+ private volatile SequenceFeature[] lastSequenceFeatures;
int sfSize;
public synchronized void drawSequence(Graphics g, final SequenceI seq,
int start, int end, int y1)
{
- SequenceFeature[] sf = seq.getSequenceFeatures();
- if (sf == null || sf.length == 0)
+ SequenceFeature[] sequenceFeatures = seq.getSequenceFeatures();
+ if (sequenceFeatures == null || sequenceFeatures.length == 0)
{
return;
}
updateFeatures();
if (lastSeq == null || seq != lastSeq
- || sf != sequenceFeatures)
+ || sequenceFeatures != lastSequenceFeatures)
{
lastSeq = seq;
- sequenceFeatures = sf;
+ lastSequenceFeatures = sequenceFeatures;
}
if (transparency != 1 && g != null)
epos = lastSeq.findPosition(end);
}
- sfSize = sequenceFeatures.length;
+ sfSize = lastSequenceFeatures.length;
String type;
for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++)
{
// current feature to render
for (sfindex = 0; sfindex < sfSize; sfindex++)
{
- if (!sequenceFeatures[sfindex].type.equals(type))
+ final SequenceFeature sequenceFeature = lastSequenceFeatures[sfindex];
+ if (!sequenceFeature.type.equals(type))
{
continue;
}
if (featureGroups != null
- && sequenceFeatures[sfindex].featureGroup != null
- && sequenceFeatures[sfindex].featureGroup.length() != 0
- && featureGroups
- .containsKey(sequenceFeatures[sfindex].featureGroup)
- && !featureGroups
- .get(sequenceFeatures[sfindex].featureGroup)
+ && sequenceFeature.featureGroup != null
+ && sequenceFeature.featureGroup.length() != 0
+ && featureGroups.containsKey(sequenceFeature.featureGroup)
+ && !featureGroups.get(sequenceFeature.featureGroup)
.booleanValue())
{
continue;
}
if (!offscreenRender
- && (sequenceFeatures[sfindex].getBegin() > epos || sequenceFeatures[sfindex]
+ && (sequenceFeature.getBegin() > epos || sequenceFeature
.getEnd() < spos))
{
continue;
if (offscreenRender && offscreenImage == null)
{
- if (sequenceFeatures[sfindex].begin <= start
- && sequenceFeatures[sfindex].end >= start)
+ if (sequenceFeature.begin <= start
+ && sequenceFeature.end >= start)
{
// this is passed out to the overview and other sequence renderers
// (e.g. molecule viewer) to get displayed colour for rendered
// sequence
- currentColour = new Integer(
- getColour(sequenceFeatures[sfindex]).getRGB());
+ currentColour = new Integer(getColour(sequenceFeature).getRGB());
// used to be retreived from av.featuresDisplayed
// currentColour = av.featuresDisplayed
// .get(sequenceFeatures[sfindex].type);
}
}
- else if (sequenceFeatures[sfindex].type.equals("disulfide bond"))
+ else if (sequenceFeature.type.equals("disulfide bond"))
{
-
- renderFeature(g, seq,
- seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
- seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
- getColour(sequenceFeatures[sfindex])
+ renderFeature(g, seq, seq.findIndex(sequenceFeature.begin) - 1,
+ seq.findIndex(sequenceFeature.begin) - 1,
+ getColour(sequenceFeature)
// new Color(((Integer) av.featuresDisplayed
// .get(sequenceFeatures[sfindex].type)).intValue())
, start, end, y1);
- renderFeature(g, seq,
- seq.findIndex(sequenceFeatures[sfindex].end) - 1,
- seq.findIndex(sequenceFeatures[sfindex].end) - 1,
- getColour(sequenceFeatures[sfindex])
+ renderFeature(g, seq, seq.findIndex(sequenceFeature.end) - 1,
+ seq.findIndex(sequenceFeature.end) - 1,
+ getColour(sequenceFeature)
// new Color(((Integer) av.featuresDisplayed
// .get(sequenceFeatures[sfindex].type)).intValue())
, start, end, y1);
}
- else if (showFeature(sequenceFeatures[sfindex]))
+ else if (showFeature(sequenceFeature))
{
if (av_isShowSeqFeatureHeight
- && sequenceFeatures[sfindex].score != Float.NaN)
+ && sequenceFeature.score != Float.NaN)
{
renderScoreFeature(g, seq,
- seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
- seq.findIndex(sequenceFeatures[sfindex].end) - 1,
- getColour(sequenceFeatures[sfindex]), start, end, y1,
- normaliseScore(sequenceFeatures[sfindex]));
+ seq.findIndex(sequenceFeature.begin) - 1,
+ seq.findIndex(sequenceFeature.end) - 1,
+ getColour(sequenceFeature), start, end, y1,
+ normaliseScore(sequenceFeature));
}
else
{
- renderFeature(g, seq,
- seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
- seq.findIndex(sequenceFeatures[sfindex].end) - 1,
- getColour(sequenceFeatures[sfindex]), start, end, y1);
+ renderFeature(g, seq, seq.findIndex(sequenceFeature.begin) - 1,
+ seq.findIndex(sequenceFeature.end) - 1,
+ getColour(sequenceFeature), start, end, y1);
}
}
*/
public class ParseHtmlBodyAndLinks
{
+ private static final Pattern LEFT_ANGLE_BRACKET_PATTERN = Pattern.compile("<");
+
String orig = null;
public String getOrig()
{
// instead of parsing the html into plaintext
// clean the description ready for embedding in html
- sb = new StringBuffer(Pattern.compile("<").matcher(description)
+ sb = new StringBuffer(LEFT_ANGLE_BRACKET_PATTERN.matcher(description)
.replaceAll("<"));
}
package jalview.util;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.regex.Pattern;
+
public class StringUtils
{
+ private static final Pattern DELIMITERS_PATTERN = Pattern.compile(".*='[^']*(?!')");
+
+ private static final boolean DEBUG = false;
/**
* Returns a new character array, after inserting characters into the given
String[] st = input.split(token);
return st[st.length - 1];
}
+
+ /**
+ * Parses the input string into components separated by the delimiter. Unlike
+ * String.split(), this method will ignore occurrences of the delimiter which
+ * are nested within single quotes in name-value pair values, e.g. a='b,c'.
+ *
+ * @param input
+ * @param delimiter
+ * @return elements separated by separator
+ */
+ public static String[] separatorListToArray(String input, String delimiter)
+ {
+ int seplen = delimiter.length();
+ if (input == null || input.equals("") || input.equals(delimiter))
+ {
+ return null;
+ }
+ List<String> jv = new ArrayList<String>();
+ int cp = 0, pos, escape;
+ boolean wasescaped = false, wasquoted = false;
+ String lstitem = null;
+ while ((pos = input.indexOf(delimiter, cp)) >= cp)
+ {
+ escape = (pos > 0 && input.charAt(pos - 1) == '\\') ? -1 : 0;
+ if (wasescaped || wasquoted)
+ {
+ // append to previous pos
+ jv.set(jv.size() - 1,
+ lstitem = lstitem + delimiter
+ + input.substring(cp, pos + escape));
+ }
+ else
+ {
+ jv.add(lstitem = input.substring(cp, pos + escape));
+ }
+ cp = pos + seplen;
+ wasescaped = escape == -1;
+ // last separator may be in an unmatched quote
+ wasquoted = DELIMITERS_PATTERN.matcher(lstitem).matches();
+ }
+ if (cp < input.length())
+ {
+ String c = input.substring(cp);
+ if (wasescaped || wasquoted)
+ {
+ // append final separator
+ jv.set(jv.size() - 1, lstitem + delimiter + c);
+ }
+ else
+ {
+ if (!c.equals(delimiter))
+ {
+ jv.add(c);
+ }
+ }
+ }
+ if (jv.size() > 0)
+ {
+ String[] v = jv.toArray(new String[jv.size()]);
+ jv.clear();
+ if (DEBUG)
+ {
+ System.err.println("Array from '" + delimiter
+ + "' separated List:\n" + v.length);
+ for (int i = 0; i < v.length; i++)
+ {
+ System.err.println("item " + i + " '" + v[i] + "'");
+ }
+ }
+ return v;
+ }
+ if (DEBUG)
+ {
+ System.err.println("Empty Array from '" + delimiter
+ + "' separated List");
+ }
+ return null;
+ }
+
+ /**
+ * Returns a string which contains the list elements delimited by the
+ * separator. Null items are ignored. If the input is null or has length zero,
+ * a single delimiter is returned.
+ *
+ * @param list
+ * @param separator
+ * @return concatenated string
+ */
+ public static String arrayToSeparatorList(String[] list, String separator)
+ {
+ StringBuffer v = new StringBuffer();
+ if (list != null && list.length > 0)
+ {
+ for (int i = 0, iSize = list.length; i < iSize; i++)
+ {
+ if (list[i] != null)
+ {
+ if (v.length() > 0)
+ {
+ v.append(separator);
+ }
+ // TODO - escape any separator values in list[i]
+ v.append(list[i]);
+ }
+ }
+ if (DEBUG)
+ {
+ System.err.println("Returning '" + separator
+ + "' separated List:\n");
+ System.err.println(v);
+ }
+ return v.toString();
+ }
+ if (DEBUG)
+ {
+ System.err.println("Returning empty '" + separator
+ + "' separated List\n");
+ }
+ return "" + separator;
+ }
}
ArrayList<SequenceFeature> tmp = new ArrayList<SequenceFeature>();
SequenceFeature[] features = sequence.getSequenceFeatures();
- while (features == null && sequence.getDatasetSequence() != null)
- {
- sequence = sequence.getDatasetSequence();
- features = sequence.getSequenceFeatures();
- }
-
if (features != null)
{
for (int i = 0; i < features.length; i++)
*/
public abstract class InputType
{
+ private static final Pattern URL_PATTERN = Pattern.compile("^([^=]+)=?'?([^']*)?'?");
+
/**
* not used yet
*/
boolean valid = true;
for (String tok : tokenstring)
{
- Matcher mtch = Pattern.compile("^([^=]+)=?'?([^']*)?'?").matcher(tok);
+ Matcher mtch = URL_PATTERN.matcher(tok);
if (mtch.find())
{
try
*/
package jalview.ws.rest;
-import jalview.datamodel.SequenceI;
-import jalview.io.packed.DataProvider.JvDataType;
-import jalview.ws.rest.params.Alignment;
-import jalview.ws.rest.params.AnnotationFile;
-import jalview.ws.rest.params.SeqGroupIndexVector;
-
import java.net.URL;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
+import jalview.datamodel.SequenceI;
+import jalview.io.packed.DataProvider.JvDataType;
+import jalview.util.StringUtils;
+import jalview.ws.rest.params.Alignment;
+import jalview.ws.rest.params.AnnotationFile;
+import jalview.ws.rest.params.SeqGroupIndexVector;
+
public class RestServiceDescription
{
+ private static final Pattern PARAM_ENCODED_URL_PATTERN = Pattern.compile("([?&])([A-Za-z0-9_]+)=\\$([^$]+)\\$");
+
/**
* create a new rest service description ready to be configured
*/
return invalidMessage == null;
}
- private static boolean debug = false;
-
- /**
- * parse the string into a list
- *
- * @param list
- * @param separator
- * @return elements separated by separator
- */
- public static String[] separatorListToArray(String list, String separator)
- {
- int seplen = separator.length();
- if (list == null || list.equals("") || list.equals(separator))
- {
- return null;
- }
- java.util.ArrayList<String> jv = new ArrayList<String>();
- int cp = 0, pos, escape;
- boolean wasescaped = false, wasquoted = false;
- String lstitem = null;
- while ((pos = list.indexOf(separator, cp)) >= cp)
- {
-
- escape = (pos > 0 && list.charAt(pos - 1) == '\\') ? -1 : 0;
- if (wasescaped || wasquoted)
- {
- // append to previous pos
- jv.set(jv.size() - 1,
- lstitem = lstitem + separator
- + list.substring(cp, pos + escape));
- }
- else
- {
- jv.add(lstitem = list.substring(cp, pos + escape));
- }
- cp = pos + seplen;
- wasescaped = escape == -1;
- // last separator may be in an unmatched quote
- wasquoted = (java.util.regex.Pattern.matches(".*='[^']*(?!')",
- lstitem));
- }
- if (cp < list.length())
- {
- String c = list.substring(cp);
- if (wasescaped || wasquoted)
- {
- // append final separator
- jv.set(jv.size() - 1, lstitem + separator + c);
- }
- else
- {
- if (!c.equals(separator))
- {
- jv.add(c);
- }
- }
- }
- if (jv.size() > 0)
- {
- String[] v = jv.toArray(new String[jv.size()]);
- jv.clear();
- if (debug)
- {
- System.err.println("Array from '" + separator
- + "' separated List:\n" + v.length);
- for (int i = 0; i < v.length; i++)
- {
- System.err.println("item " + i + " '" + v[i] + "'");
- }
- }
- return v;
- }
- if (debug)
- {
- System.err.println("Empty Array from '" + separator
- + "' separated List");
- }
- return null;
- }
-
- /**
- * concatenate the list with separator
- *
- * @param list
- * @param separator
- * @return concatenated string
- */
- public static String arrayToSeparatorList(String[] list, String separator)
- {
- StringBuffer v = new StringBuffer();
- if (list != null && list.length > 0)
- {
- for (int i = 0, iSize = list.length; i < iSize; i++)
- {
- if (list[i] != null)
- {
- if (v.length() > 0)
- {
- v.append(separator);
- }
- // TODO - escape any separator values in list[i]
- v.append(list[i]);
- }
- }
- if (debug)
- {
- System.err.println("Returning '" + separator
- + "' separated List:\n");
- System.err.println(v);
- }
- return v.toString();
- }
- if (debug)
- {
- System.err.println("Returning empty '" + separator
- + "' separated List\n");
- }
- return "" + separator;
- }
-
/**
* parse a string containing a list of service properties and configure the
* service description
private boolean configureFromServiceInputProperties(String propList,
StringBuffer warnings)
{
- String[] props = separatorListToArray(propList, ",");
+ String[] props = StringUtils.separatorListToArray(propList, ",");
if (props == null)
{
return true;
;
vls.add(new String("gapCharacter='" + gapCharacter + "'"));
vls.add(new String("returns='" + _genOutputFormatString() + "'"));
- return arrayToSeparatorList(vls.toArray(new String[0]), ",");
+ return StringUtils.arrayToSeparatorList(vls.toArray(new String[0]), ",");
}
public String toString()
public boolean configureFromEncodedString(String encoding,
StringBuffer warnings)
{
- String[] list = separatorListToArray(encoding, "|");
+ String[] list = StringUtils.separatorListToArray(encoding, "|");
int nextpos = parseServiceList(list, warnings, 0);
if (nextpos > 0)
url.append("$");
url.append(param.getValue().getURLtokenPrefix());
url.append(":");
- url.append(arrayToSeparatorList(vals.toArray(new String[0]),
+ url.append(StringUtils.arrayToSeparatorList(vals.toArray(new String[0]),
","));
url.append("$");
}
boolean valid = true;
int lastp = 0;
String url = new String();
- Matcher prms = Pattern.compile("([?&])([A-Za-z0-9_]+)=\\$([^$]+)\\$")
+ Matcher prms = PARAM_ENCODED_URL_PATTERN
.matcher(ipurl);
Map<String, InputType> iparams = new Hashtable<String, InputType>();
InputType jinput;
if (iprm.equalsIgnoreCase(jinput.getURLtokenPrefix()))
{
ArrayList<String> al = new ArrayList<String>();
- for (String prprm : separatorListToArray(iprmparams, ","))
+ for (String prprm : StringUtils.separatorListToArray(iprmparams, ","))
{
// hack to ensure that strings like "sep=','" containing unescaped
// commas as values are concatenated
public static List<RestServiceDescription> parseDescriptions(
String services) throws Exception
{
- String[] list = separatorListToArray(services, "|");
+ String[] list = StringUtils.separatorListToArray(services, "|");
List<RestServiceDescription> svcparsed = new ArrayList<RestServiceDescription>();
int p = 0, lastp = 0;
StringBuffer warnings = new StringBuffer();
assertEquals("zABCDEF", seq.getSequenceAsString());
seq.insertCharAt(2, 2, 'x');
assertEquals("zAxxBCDEF", seq.getSequenceAsString());
-
// for static method see StringUtilsTest
}
package jalview.ext.paradise;
import static org.junit.Assert.assertTrue;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SequenceI;
-import jalview.io.FastaFile;
-import jalview.io.FormatAdapter;
import java.io.BufferedReader;
import java.io.File;
import org.junit.Test;
import MCview.PDBfile;
-
import compbio.util.FileUtil;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+import jalview.io.FastaFile;
+import jalview.io.FormatAdapter;
+
public class TestAnnotate3D
{
sb.append(line + "\n");
}
assertTrue("No data returned by Annotate3D", sb.length() > 0);
- AlignmentI al = new FormatAdapter().readFile(sb.toString(),
+ final String lines = sb.toString();
+ AlignmentI al = new FormatAdapter().readFile(lines,
FormatAdapter.PASTE, "RNAML");
if (al == null || al.getHeight() == 0)
{
- System.out.println(sb.toString());
+ System.out.println(lines);
}
assertTrue("No alignment returned.", al != null);
assertTrue("No sequences in returned alignment.", al.getHeight() > 0);
String sq_ = new String(sq.getSequence()).toLowerCase();
for (SequenceI _struseq : pdbf.getSeqsAsArray())
{
- if (new String(_struseq.getSequence()).toLowerCase().equals(
+ final String lowerCase = new String(_struseq.getSequence()).toLowerCase();
+ if (lowerCase.equals(
sq_))
{
struseq = _struseq;
}
/**
- * Test mapping a column selection including hidden columns
- *
- * @throws IOException
- */
- @Test
- public void testMapColumnSelection_hiddenColumns() throws IOException
- {
- setupMappedAlignments();
-
- ColumnSelection colsel = new ColumnSelection();
-
- /*
- * Column 0 in protein picks up Seq2/L, Seq3/G which map to cols 0-4 and 0-3
- * in dna respectively, overall 0-4
- */
- colsel.addElement(0);
- ColumnSelection cs = MappingUtils.mapColumnSelection(colsel,
- proteinView, dnaView);
- assertEquals("[0, 1, 2, 3, 4]", cs.getSelected().toString());
-
- fail("write me");
- }
-
- /**
* Test mapping a column selection in dna to its protein equivalent
*
* @throws IOException
assertEquals("file1.dat", StringUtils.getLastToken(
"file://localhost:8080/data/examples/file1.dat", "/"));
}
+
+ @Test
+ public void testSeparatorListToArray()
+ {
+ String[] result = StringUtils.separatorListToArray(
+ "foo=',',min='foo',max='1,2,3',fa=','", ",");
+ assertEquals("[foo=',', min='foo', max='1,2,3', fa=',']",
+ Arrays.toString(result));
+ /*
+ * Comma nested in '' is not treated as delimiter; tokens are not trimmed
+ */
+ result = StringUtils.separatorListToArray("minsize='2', sep=','", ",");
+ assertEquals("[minsize='2', sep=',']", Arrays.toString(result));
+
+ /*
+ * String delimited by | containing a quoted | (should not be treated as
+ * delimiter)
+ */
+ assertEquals("[abc='|'d, ef, g]", Arrays.toString(StringUtils
+ .separatorListToArray("abc='|'d|ef|g", "|")));
+ }
+
+ @Test
+ public void testArrayToSeparatorList()
+ {
+ assertEquals("*", StringUtils.arrayToSeparatorList(null, "*"));
+ assertEquals("*", StringUtils.arrayToSeparatorList(new String[]
+ {}, "*"));
+ assertEquals("a*bc*cde", StringUtils.arrayToSeparatorList(new String[]
+ { "a", "bc", "cde" }, "*"));
+ assertEquals("a*cde", StringUtils.arrayToSeparatorList(new String[]
+ { "a", null, "cde" }, "*"));
+ assertEquals("a**cde", StringUtils.arrayToSeparatorList(new String[]
+ { "a", "", "cde" }, "*"));
+ // delimiter within token is not (yet) escaped
+ assertEquals("a*b*c*cde", StringUtils.arrayToSeparatorList(new String[]
+ { "a", "b*c", "cde" }, "*"));
+ }
}
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
-import jalview.datamodel.AlignmentI;
-import jalview.gui.Jalview2XML;
-import jalview.io.AnnotationFile;
-import jalview.io.FormatAdapter;
-import jalview.io.StockholmFileTest;
-import jalview.ws.jws2.JPred301Client;
-import jalview.ws.jws2.JabaParamStore;
-import jalview.ws.jws2.Jws2Discoverer;
-import jalview.ws.jws2.SequenceAnnotationWSClient;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
-import jalview.ws.params.AutoCalcSetting;
import java.awt.Component;
import java.util.ArrayList;
import compbio.metadata.Argument;
import compbio.metadata.WrongParameterException;
+import jalview.datamodel.AlignmentI;
+import jalview.gui.Jalview2XML;
+import jalview.io.AnnotationFile;
+import jalview.io.FormatAdapter;
+import jalview.io.StockholmFileTest;
+import jalview.ws.jws2.JPred301Client;
+import jalview.ws.jws2.JabaParamStore;
+import jalview.ws.jws2.Jws2Discoverer;
+import jalview.ws.jws2.SequenceAnnotationWSClient;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.AutoCalcSetting;
+
public class JpredJabaStructExportImport
{
public static String testseqs = "examples/uniref50.fa";
if (jpredws == null)
{
- System.exit(0);
+ fail("jpredws is null");
}
jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
-import jalview.datamodel.AlignmentI;
-import jalview.gui.Jalview2XML;
-import jalview.io.AnnotationFile;
-import jalview.io.FormatAdapter;
-import jalview.io.StockholmFileTest;
-import jalview.ws.jws2.Jws2Discoverer;
-import jalview.ws.jws2.RNAalifoldClient;
-import jalview.ws.jws2.SequenceAnnotationWSClient;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
-import jalview.ws.params.AutoCalcSetting;
import java.awt.Component;
import java.util.ArrayList;
import compbio.metadata.WrongParameterException;
+import jalview.datamodel.AlignmentI;
+import jalview.gui.Jalview2XML;
+import jalview.io.AnnotationFile;
+import jalview.io.FormatAdapter;
+import jalview.io.StockholmFileTest;
+import jalview.ws.jws2.Jws2Discoverer;
+import jalview.ws.jws2.RNAalifoldClient;
+import jalview.ws.jws2.SequenceAnnotationWSClient;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.AutoCalcSetting;
+
public class RNAStructExportImport
{
public static String testseqs = "examples/unfolded_RF00031.aln";
if (rnaalifoldws == null)
{
- System.exit(0);
+ fail("no web service");
}
jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
*/
package jalview.ws.rest;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
-import java.io.BufferedReader;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Hashtable;
-import java.util.List;
import java.util.Map;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.AlignmentView;
-import jalview.gui.AlignFrame;
-import jalview.io.FileParse;
-import jalview.ws.rest.InputType;
-import jalview.ws.rest.params.SeqGroupIndexVector;
-
-import org.junit.AfterClass;
-import org.junit.BeforeClass;
import org.junit.Test;
+import jalview.gui.AlignFrame;
+import jalview.util.StringUtils;
+
/**
* @author jimp
*
{
@Test
- public void testSeparatorListToArrayForRestServiceDescriptions()
- {
- assertTrue(
- "separatorListToArray is faulty.",
- RestServiceDescription.separatorListToArray(
- "foo=',',min='foo',max='1,2,3',fa=','", ",").length == 4);
- assertTrue("separatorListToArray is faulty.",
- RestServiceDescription.separatorListToArray(
- "minsize='2', sep=','", ",").length != 2); // probably
- // should come as
- // 2
- }
-
- @Test
public void testShmmrService()
{
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
-import jalview.analysis.CrossRef;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.DBRefSource;
-import jalview.util.DBRefUtils;
-import jalview.ws.SequenceFetcher;
import java.util.ArrayList;
import java.util.List;
import org.junit.BeforeClass;
import org.junit.Test;
+import jalview.analysis.CrossRef;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.util.DBRefUtils;
+import jalview.ws.SequenceFetcher;
+
/**
* @author jimp
*
git://source.jalview.org / jalview.git / commitdiff