From: Jim Procter Date: Mon, 7 Feb 2022 12:13:26 +0000 (+0000) Subject: JAL-722 updated from 2.11.2 develop branch - needs further work before release X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=48a66195bf4aee8b2c479d3bbbf4c1fb8b824f5a;hp=4d71acba1cc4999e8e4061ec3e9ae55e1b37084e;p=jalview.git JAL-722 updated from 2.11.2 develop branch - needs further work before release Conflicts: resources/lang/Messages.properties resources/lang/Messages_es.properties src/jalview/datamodel/Alignment.java src/jalview/gui/AlignFrame.java src/jalview/io/AlignFile.java src/jalview/project/Jalview2XML.java --- diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties index b448b4c..075cb18 100644 --- a/resources/lang/Messages.properties +++ b/resources/lang/Messages.properties @@ -317,7 +317,6 @@ label.removed_columns = Removed {0} columns. label.removed_empty_columns = Removed {0} empty columns. label.paste_newick_tree_file = Paste your Newick tree file here. label.order_by_params = Order by {0} -label.html_content = {0} label.paste_pdb_file= Paste your PDB file here. label.paste_pdb_file_for_sequence = Paste PDB file for sequence {0} label.could_not_parse_newick_file = Could not parse Newick file\!\n {0} @@ -948,6 +947,7 @@ error.implementation_error_old_jalview_object_not_bound =IMPLEMENTATION ERROR: o error.implementation_error_vamsas_doc_class_should_bind_to_type = Implementation Error: Vamsas Document Class {0} should bind to a {1} (found a {2}) error.invalid_vamsas_rangetype_cannot_resolve_lists = Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice! error.implementation_error_cannot_have_null_alignment = Implementation error: Cannot have null alignment property key +error.implementation_error_maplist_is_null = Implementation error. MapList is null for initMapType. error.implementation_error_null_fileparse = Implementation error. Null FileParse in copy constructor error.implementation_error_structure_selection_manager_null = Implementation error. Structure selection manager's context is 'null' exception.ssm_context_is_null = SSM context is null diff --git a/resources/lang/Messages_es.properties b/resources/lang/Messages_es.properties index 49e05e3..404a157 100644 --- a/resources/lang/Messages_es.properties +++ b/resources/lang/Messages_es.properties @@ -282,7 +282,6 @@ label.removed_columns = {0} columnas eliminadas. label.removed_empty_columns = {0} columnas vacías eliminadas. label.paste_newick_tree_file = Pegar su fichero árbol Newick aquí. label.order_by_params = Ordenar por {0} -label.html_content = {0} label.paste_pdb_file= Pegar tu fichero PDB aquí. label.paste_pdb_file_for_sequence = Pegar fichero PDB para la secuencia {0} label.could_not_parse_newick_file = No se pudo analizar el fichero Newick\!\n {0} @@ -866,6 +865,7 @@ error.implementation_error_old_jalview_object_not_bound =Error de implementaci error.implementation_error_vamsas_doc_class_should_bind_to_type = Error de implementación: la clase de documento VAMSAS {0} debe enlazar a {1} (pero se ha encontrado que lo está a {2}) error.invalid_vamsas_rangetype_cannot_resolve_lists = RangeType VAMSAS no válido - ¡no es posible resolver ambas listas de Pos y Seg con los valores elegidos! error.implementation_error_cannot_have_null_alignment = Error de implementación: no es posible tener una clave nula en el alineamiento +error.implementation_error_maplist_is_null = Error de implementación. MapList es nulo en initMapType. error.implementation_error_null_fileparse = Error de implementación. FileParse nulo en el construictor de copia error.implementation_error_structure_selection_manager_null = Error de implementación. El contexto structure selection manager's es nulo exception.ssm_context_is_null = El contexto SSM es nulo diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java index 80db11d..713ae02 100644 --- a/src/jalview/appletgui/APopupMenu.java +++ b/src/jalview/appletgui/APopupMenu.java @@ -911,9 +911,7 @@ public class APopupMenu extends java.awt.PopupMenu ? sequences[0].getDisplayId(true) : "Selection"), 600, 500); - cap.setText( - MessageManager.formatMessage("label.html_content", new Object[] - { contents.toString() })); + cap.setText("" + contents.toString() + ""); } void editName() diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index b6f8929..eb6b863 100644 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -51,6 +51,7 @@ import jalview.datamodel.PDBEntry; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; +import jalview.io.AlignmentProperties; import jalview.io.AnnotationFile; import jalview.io.AppletFormatAdapter; import jalview.io.DataSourceType; @@ -1208,7 +1209,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } else if (source == alProperties) { - StringBuffer contents = new jalview.io.AlignmentProperties( + StringBuilder contents = new AlignmentProperties( viewport.getAlignment()).formatAsString(); CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this); cap.setText(contents.toString()); diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java index c4098e2..310847b 100755 --- a/src/jalview/datamodel/Alignment.java +++ b/src/jalview/datamodel/Alignment.java @@ -32,8 +32,8 @@ import java.util.Arrays; import java.util.BitSet; import java.util.Collections; import java.util.Enumeration; +import java.util.HashMap; import java.util.HashSet; -import java.util.Hashtable; import java.util.Iterator; import java.util.List; import java.util.Map; @@ -67,7 +67,7 @@ public class Alignment implements AlignmentI, AutoCloseable HiddenColumns hiddenCols; - public Hashtable alignmentProperties; + public Map alignmentProperties; private List codonFrameList; @@ -1371,7 +1371,7 @@ public class Alignment implements AlignmentI, AutoCloseable { if (alignmentProperties == null) { - alignmentProperties = new Hashtable(); + alignmentProperties = new HashMap<>(); } alignmentProperties.put(key, value); @@ -1391,7 +1391,7 @@ public class Alignment implements AlignmentI, AutoCloseable } @Override - public Hashtable getProperties() + public Map getProperties() { return alignmentProperties; } @@ -1559,10 +1559,10 @@ public class Alignment implements AlignmentI, AutoCloseable { // we really can't do very much here - just try to concatenate strings // where property collisions occur. - Enumeration key = toappend.getProperties().keys(); - while (key.hasMoreElements()) + Iterator key = toappend.getProperties().keySet().iterator(); + while (key.hasNext()) { - Object k = key.nextElement(); + Object k = key.next(); Object ourval = this.getProperty(k); Object toapprop = toappend.getProperty(k); if (ourval != null) diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java index 93a2456..4b1220b 100755 --- a/src/jalview/datamodel/AlignmentI.java +++ b/src/jalview/datamodel/AlignmentI.java @@ -20,7 +20,6 @@ */ package jalview.datamodel; -import java.util.Hashtable; import java.util.List; import java.util.Map; import java.util.Set; @@ -403,7 +402,7 @@ public interface AlignmentI extends AnnotatedCollectionI * * @return hashtable of alignment properties (or null if none are defined) */ - Hashtable getProperties(); + Map getProperties(); /** * add a reference to a frame of aligned codons for this alignment diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 8deff01..a36c186 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -3379,49 +3379,42 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } @Override - public void alignmentProperties() - { - JComponent pane; - StringBuffer contents = new AlignmentProperties(viewport.getAlignment()) - - .formatAsHtml(); - String content = MessageManager.formatMessage("label.html_content", - new Object[] - { contents.toString() }); - contents = null; - - if (Platform.isJS()) - { - JLabel textLabel = new JLabel(); - textLabel.setText(content); - textLabel.setBackground(Color.WHITE); - - pane = new JPanel(new BorderLayout()); - ((JPanel) pane).setOpaque(true); - pane.setBackground(Color.WHITE); - ((JPanel) pane).add(textLabel, BorderLayout.NORTH); - } - else - /** - * Java only - * - * @j2sIgnore - */ - { - JEditorPane editPane = new JEditorPane("text/html", ""); - editPane.setEditable(false); - editPane.setText(content); - pane = editPane; - } - - JInternalFrame frame = new JInternalFrame(); - - frame.getContentPane().add(new JScrollPane(pane)); - - Desktop.addInternalFrame(frame, MessageManager - .formatMessage("label.alignment_properties", new Object[] - { getTitle() }), 500, 400); - } + public void alignmentProperties() { + JComponent pane; + StringBuilder contents = new StringBuilder(128); + contents.append(""); + contents.append(new AlignmentProperties(viewport.getAlignment()).formatAsHtml()); + contents.append(""); + + String content = contents.toString(); + + JInternalFrame frame = null; + if (Platform.isJS()) { + JLabel textLabel = new JLabel(); + textLabel.setText(content); + textLabel.setBackground(Color.WHITE); + + pane = new JPanel(new BorderLayout()); + ((JPanel) pane).setOpaque(true); + pane.setBackground(Color.WHITE); + ((JPanel) pane).add(textLabel, BorderLayout.NORTH); + frame = new JInternalFrame(); + frame.getContentPane().add(new JScrollPane(pane)); + } else + /** + * Java only + * + * @j2sIgnore + */ + { + CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer(); + cap.setText(content); + frame = cap; + } + + Desktop.addInternalFrame(frame, + MessageManager.formatMessage("label.alignment_properties", new Object[] { getTitle() }), 500, 400); + } /** * DOCUMENT ME! diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java index 3202ac9..48f65cf 100755 --- a/src/jalview/io/AlignFile.java +++ b/src/jalview/io/AlignFile.java @@ -22,9 +22,10 @@ package jalview.io; import java.io.IOException; import java.util.ArrayList; -import java.util.Enumeration; import java.util.Hashtable; import java.util.List; +import java.util.Map; +import java.util.Map.Entry; import java.util.Vector; import jalview.datamodel.AlignmentAnnotation; @@ -66,7 +67,7 @@ public abstract class AlignFile extends FileParse /** * Properties to be added to generated alignment object */ - private Hashtable properties; + private Map properties; long start; @@ -288,13 +289,11 @@ public abstract class AlignFile extends FileParse */ public void addProperties(AlignmentI al) { - if (properties != null && properties.size() > 0) + if (properties != null) { - Enumeration keys = properties.keys(); - Enumeration vals = properties.elements(); - while (keys.hasMoreElements()) + for (Entry prop : properties.entrySet()) { - al.setProperty(keys.nextElement(), vals.nextElement()); + al.setProperty(prop.getKey(), prop.getValue()); } } } @@ -309,12 +308,12 @@ public abstract class AlignFile extends FileParse * @param value * - non-null value */ - protected void setAlignmentProperty(Object key, Object value) + protected void setAlignmentProperty(String key, String value) { if (key == null) { - throw new Error(MessageManager.getString( - "error.implementation_error_cannot_have_null_alignment")); + throw new Error( + "Implementation error: Cannot have null alignment property key."); } if (value == null) { @@ -322,12 +321,12 @@ public abstract class AlignFile extends FileParse } if (properties == null) { - properties = new Hashtable(); + properties = new Hashtable<>(); } properties.put(key, value); } - protected Object getAlignmentProperty(Object key) + protected String getAlignmentProperty(String key) { if (properties != null && key != null) { @@ -341,9 +340,9 @@ public abstract class AlignFile extends FileParse */ protected void initData() { - seqs = new Vector(); - annotations = new Vector(); - seqGroups = new ArrayList(); + seqs = new Vector<>(); + annotations = new Vector<>(); + seqGroups = new ArrayList<>(); parseCalled = false; } @@ -356,7 +355,7 @@ public abstract class AlignFile extends FileParse @Override public void setSeqs(SequenceI[] s) { - seqs = new Vector(); + seqs = new Vector<>(); for (int i = 0; i < s.length; i++) { @@ -427,7 +426,7 @@ public abstract class AlignFile extends FileParse { if (newickStrings == null) { - newickStrings = new Vector(); + newickStrings = new Vector<>(); } newickStrings.addElement(new String[] { treeName, newickString }); } diff --git a/src/jalview/io/AlignmentProperties.java b/src/jalview/io/AlignmentProperties.java index f2a6150..69bd658 100644 --- a/src/jalview/io/AlignmentProperties.java +++ b/src/jalview/io/AlignmentProperties.java @@ -20,13 +20,12 @@ */ package jalview.io; -import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; +import jalview.datamodel.SequenceI; -import java.io.PrintWriter; -import java.io.StringWriter; -import java.util.Enumeration; -import java.util.Hashtable; +import java.util.Arrays; +import java.util.Comparator; +import java.util.Map; /** * Render associated attributes of an alignment. The heart of this code was @@ -37,6 +36,12 @@ import java.util.Hashtable; */ public class AlignmentProperties { + private static final String BR_TAG = "
"; + + private static final String NEWLINE = System.getProperty("line.separator"); + + private static final String PCT_FORMAT = "%.1f%%"; + AlignmentI alignment; public AlignmentProperties(AlignmentI alignment) @@ -47,100 +52,172 @@ public class AlignmentProperties /** * render the alignment's properties report as text or an HTML fragment * - * @param pw * @param html */ - public void writeProperties(PrintWriter pw, boolean html) + protected StringBuilder writeProperties(boolean html) { - final String nl = html ? "
" : System.getProperty("line.separator"); - float avg = 0; - int min = Integer.MAX_VALUE, max = 0; - for (int i = 0; i < alignment.getHeight(); i++) + StringBuilder sb = new StringBuilder(256); + final String nl = html ? BR_TAG : NEWLINE; + int totalLength = 0; + int totalGaps = 0; + int minLength = Integer.MAX_VALUE; + int maxLength = 0; + float maxUngapped = 0f; + float minUngapped = Float.MAX_VALUE; + + final int height = alignment.getHeight(); + final int width = alignment.getWidth(); + + for (int i = 0; i < height; i++) { - int size = 1 + alignment.getSequenceAt(i).getEnd() - - alignment.getSequenceAt(i).getStart(); - avg += size; - if (size > max) - { - max = size; - } - if (size < min) - { - min = size; - } + SequenceI seq = alignment.getSequenceAt(i); + // sequence length including gaps: + int seqWidth = seq.getLength(); + // sequence length excluding gaps: + int seqLength = 1 + seq.getEnd() - seq.getStart(); + int gapCount = seqWidth - seqLength; // includes padding + totalLength += seqLength; + totalGaps += gapCount; + maxLength = Math.max(maxLength, seqLength); + minLength = Math.min(minLength, seqLength); + + /* + * proportion of aligned sequence that is ungapped + * (note: normalised by alignment width here) + */ + float ungapped = (seqWidth - gapCount) / (float) seqWidth; + maxUngapped = Math.max(maxUngapped, ungapped); + minUngapped = Math.min(minUngapped, ungapped); } - avg = avg / alignment.getHeight(); - pw.print(nl); - pw.print("Sequences: " + alignment.getHeight()); - pw.print(nl); - pw.print("Minimum Sequence Length: " + min); - pw.print(nl); - pw.print("Maximum Sequence Length: " + max); - pw.print(nl); - pw.print("Average Length: " + (int) avg); - - if (((Alignment) alignment).alignmentProperties != null) + float avgLength = totalLength / (float) height; + + sb.append(html ? "" : nl); + appendRow(sb, "Sequences", String.valueOf(height), html); + appendRow(sb, "Alignment width", String.valueOf(width), + html); + appendRow(sb, "Minimum Sequence Length", String.valueOf(minLength), + html); + appendRow(sb, "Maximum Sequence Length", String.valueOf(maxLength), + html); + appendRow(sb, "Average Length", String.valueOf((int) avgLength), html); + appendRow(sb, "Minimum (sequence length / width)", + String.format(PCT_FORMAT, minUngapped * 100f), html); + appendRow(sb, "Maximum (sequence length / width)", + String.format(PCT_FORMAT, maxUngapped * 100f), html); + appendRow(sb, "Residue density", String.format(PCT_FORMAT, + (height * width - totalGaps) * 100f / (height * width)), html); + appendRow(sb, "Gap density", + String.format(PCT_FORMAT, totalGaps * 100f / (height * width)), + html); + sb.append(html ? "
" : nl); + + Map props = alignment.getProperties(); + if (props != null && !props.isEmpty()) { - pw.print(nl); - pw.print(nl); + sb.append(nl); + sb.append(nl); if (html) { - pw.print(""); + sb.append("
"); } - Hashtable props = ((Alignment) alignment).alignmentProperties; - Enumeration en = props.keys(); - while (en.hasMoreElements()) + + /* + * sort keys alphabetically for ease of reading the output + */ + Object[] keys = props.keySet().toArray(new Object[props.size()]); + Arrays.sort(keys, new Comparator() { - String key = en.nextElement().toString(); - String vals = props.get(key).toString(); - if (html) + @Override + public int compare(Object o1, Object o2) { - // wrap the text in the table - StringBuffer val = new StringBuffer(); - int pos = 0, npos; - do - { - npos = vals.indexOf("\n", pos); - if (npos == -1) - { - val.append(vals.substring(pos)); - } - else - { - val.append(vals.substring(pos, npos)); - val.append("
"); - } - pos = npos + 1; - } while (npos != -1); - pw.print(""); + return String.CASE_INSENSITIVE_ORDER.compare(o1.toString(), + o2.toString()); } - else + }); + for (Object key : keys) + { + String value = props.get(key).toString(); + if (html) { - pw.print(nl + key + "\t" + vals); + value = value.replaceAll("\\R", value); // Java 8 newline matcher + value = formatHrefs(value); } + appendRow(sb, key.toString(), value, html); } if (html) { - pw.print("
" + key + "" + val + "
"); + sb.append(""); } } + return sb; } /** - * generate a report as plain text + * Helper method to change any token starting with http into an html href * + * @param value * @return */ - public StringBuffer formatAsString() + private String formatHrefs(String value) + { + if (!value.contains("http")) + { + return value; + } + + StringBuilder sb = new StringBuilder(value.length() * 3); + String[] tokens = value.split("\\s"); + boolean found = false; + boolean first = true; + for (String token : tokens) + { + if (token.startsWith("http")) + { + token = "" + token + ""; + found = true; + } + if (!first) + { + sb.append(" "); + } + sb.append(token); + first = false; + } + return found ? sb.toString() : value; + } + + /** + * A helper method to add one key-value row, optionally in HTML table entry + * format + * + * @param sb + * @param key + * @param value + * @param html + */ + private void appendRow(StringBuilder sb, String key, String value, + boolean html) { - return formatReport(false); + if (html) + { + sb.append("").append(key).append("").append(value) + .append(""); + } + else + { + sb.append(html ? BR_TAG : NEWLINE).append(key).append("\t") + .append(value); + } } - protected StringBuffer formatReport(boolean html) + /** + * generate a report as plain text + * + * @return + */ + public StringBuilder formatAsString() { - StringWriter content = new StringWriter(); - writeProperties(new PrintWriter(content), html); - return content.getBuffer(); + return writeProperties(false); } /** @@ -148,9 +225,9 @@ public class AlignmentProperties * * @return */ - public StringBuffer formatAsHtml() + public StringBuilder formatAsHtml() { - return formatReport(true); + return writeProperties(true); } } diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java index 934be41..64204b4 100755 --- a/src/jalview/io/AnnotationFile.java +++ b/src/jalview/io/AnnotationFile.java @@ -134,8 +134,8 @@ public class AnnotationFile * @return annotation file */ public String printAnnotations(AlignmentAnnotation[] annotations, - List list, Hashtable properties, HiddenColumns cs, - AlignmentI al, ViewDef view) + List list, Map properties, + HiddenColumns cs, AlignmentI al, ViewDef view) { if (view != null) { @@ -439,14 +439,13 @@ public class AnnotationFile text.append(newline); text.append(newline); text.append("ALIGNMENT"); - Enumeration en = properties.keys(); - while (en.hasMoreElements()) + for (Object ko : properties.keySet()) { - String key = en.nextElement().toString(); + String key = ko.toString(); text.append("\t"); text.append(key); text.append("="); - text.append(properties.get(key)); + text.append(properties.get(ko)); } // TODO: output alignment visualization settings here if required // iterate through one or more views, defining, marking columns and rows diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java index c8c9c8a..9ca86f2 100644 --- a/src/jalview/io/StockholmFile.java +++ b/src/jalview/io/StockholmFile.java @@ -34,6 +34,7 @@ import java.util.Hashtable; import java.util.LinkedHashMap; import java.util.List; import java.util.Map; +import java.util.Map.Entry; import java.util.Vector; import com.stevesoft.pat.Regex; @@ -1009,15 +1010,11 @@ public class StockholmFile extends AlignFile // output database type if (al.getProperties() != null) { - if (!al.getProperties().isEmpty()) + for (Entry prop : al.getProperties().entrySet()) { - Enumeration key = al.getProperties().keys(); - Enumeration val = al.getProperties().elements(); - while (key.hasMoreElements()) - { - out.append("#=GF " + key.nextElement() + " " + val.nextElement()); - out.append(newline); - } + out.append("#=GF " + prop.getKey().toString() + " " + + prop.getValue().toString()); + out.append(newline); } } diff --git a/src/jalview/jbgui/GUserDefinedColours.java b/src/jalview/jbgui/GUserDefinedColours.java index 359f787..5c000dd 100755 --- a/src/jalview/jbgui/GUserDefinedColours.java +++ b/src/jalview/jbgui/GUserDefinedColours.java @@ -208,10 +208,9 @@ public class GUserDefinedColours extends JPanel label.setFont(new java.awt.Font("Verdana", Font.ITALIC, 10)); label.setOpaque(false); label.setPreferredSize(new Dimension(260, 34)); - label.setText( - MessageManager.formatMessage("label.html_content", new String[] - { MessageManager.getString( - "label.save_colour_scheme_with_unique_name_added_to_colour_menu") })); + label.setText("" + MessageManager.getString( + "label.save_colour_scheme_with_unique_name_added_to_colour_menu") + + ""); caseSensitive.setText(MessageManager.getString("label.case_sensitive")); caseSensitive.addActionListener(new ActionListener() { @@ -260,7 +259,7 @@ public class GUserDefinedColours extends JPanel { choosers[0] }); } - selectedButtons = new ArrayList(); + selectedButtons = new ArrayList<>(); } /** diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java index acfeb2a..985aece 100644 --- a/src/jalview/project/Jalview2XML.java +++ b/src/jalview/project/Jalview2XML.java @@ -914,13 +914,12 @@ public class Jalview2XML } if (jal.getProperties() != null) { - Enumeration en = jal.getProperties().keys(); - while (en.hasMoreElements()) + for (Entry prop : jal.getProperties().entrySet()) { - String key = en.nextElement().toString(); + String key = prop.getKey().toString(); SequenceSetProperties ssp = new SequenceSetProperties(); ssp.setKey(key); - ssp.setValue(jal.getProperties().get(key).toString()); + ssp.setValue(prop.getValue().toString()); // vamsasSet.addSequenceSetProperties(ssp); vamsasSet.getSequenceSetProperties().add(ssp); } diff --git a/test/jalview/io/AlignmentPropertiesTest.java b/test/jalview/io/AlignmentPropertiesTest.java new file mode 100644 index 0000000..a3f58ce --- /dev/null +++ b/test/jalview/io/AlignmentPropertiesTest.java @@ -0,0 +1,36 @@ +package jalview.io; + +import static org.testng.Assert.assertEquals; + +import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceI; + +import org.testng.annotations.Test; + +public class AlignmentPropertiesTest +{ + @Test(groups="Functional") + public void testWriteProperties_asHtml() + { + SequenceI seq1 = new Sequence("Seq1", "--ABC-DEFGH-"); // 8 residues + SequenceI seq2 = new Sequence("Seq2", "---BC-DE-KH-"); // 6 + SequenceI seq3 = new Sequence("Seq3", "-RABCFDE-KH-"); // 9 + AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2, seq3 }); + + AlignmentProperties ap = new AlignmentProperties(al); + StringBuilder sb = ap.writeProperties(true); + String expected = "" + + "" + + "" + + "" + + "" + + "" + + "" // 6/12 + + "" // 9/12 + + "" // 23/36 + + "" + "
Sequences3
Alignment width12
Minimum Sequence Length6
Maximum Sequence Length9
Average Length7
Minimum (sequence length / width)50.0%
Maximum (sequence length / width)75.0%
Residue density63.9%
Gap density36.1%
"; + assertEquals(sb.toString(), expected); + } +}