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cariann09cariann09
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‎java/src/circview/ControlPanelCirc.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -56,7 +56,7 @@ public ControlPanelCirc(CircPanel _cp, HelpBar _hb)
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helpButton = (JButton) Utilities.createButton(this,"/images/help.gif","Help: Online documentation." ,hb,null,false);
5757
helpButton.addActionListener(new ActionListener() {
5858
public void actionPerformed(ActionEvent e) {
59-
String url = SyMAP.USER_GUIDE_URL;
59+
String url = SyMAP.USER_GUIDE_URL + SyMAP.circle; // CAS510
6060
if ( !Utilities.tryOpenURL(url) )
6161
System.err.println("Error opening URL: " + url);
6262
}

‎java/src/dotplot/ControlPanel.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -69,7 +69,7 @@ public void stateChanged(ChangeEvent e) {
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helpButton.addActionListener(new ActionListener() {
7171
public void actionPerformed(ActionEvent e) {
72-
String url = SyMAP.USER_GUIDE_URL + "#dotplot_display";
72+
String url = SyMAP.USER_GUIDE_URL + SyMAP.dotplot; // CAS510
7373
if ( !Utilities.tryOpenURL(url) )
7474
System.err.println("Error opening URL: " + url);
7575
}

‎java/src/html/ProjManagerHelp.html‎

Lines changed: 41 additions & 31 deletions
Original file line numberDiff line numberDiff line change
@@ -2,54 +2,60 @@
22
<body style="padding:20px;font-family:arial;">
33
<h2>Summary Section</h2>
44

5-
65
<div style="width:500px">
76
The projects selected from the <b>Projects</b> in
8-
the left panel are listed in this Summary Section.
7+
the left panel are listed in this Summary Section.
98
The possible functions vary with the state, as listed below:
109

1110
<table border='1' cellpadding='5' rules=all>
1211
<tr><td><b>Function</b><td><b>Description</b>
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1413
<tr><td colspan=2><i>If there is any project not loaded to the database, you will see:</i>
15-
<tr><td valign=top>Load All Projects<td valign=top>Load all projects that have not been loaded yet.
14+
<tr><td valign=top>Load All Projects<td valign=top>Load all projects that have not been loaded yet.
1615

1716
<tr><td colspan=2><i>If a project <b>is not</b> loaded to the database, you will see:</i>
1817
<tr><td valign=top>Remove from disk<td valign=top>Remove your files from disk. The project will no longer be shown on the left.
19-
<tr><td valign=top>Load project<td valign=top>Loads the sequence and optional annotations to the database.
18+
<tr><td valign=top>Load project<td valign=top>Loads the sequence and optional annotations to the database.
2019
<tr><td valign=top>Parameters<td valign=top>This brings up a panel of parameters.
2120
Make sure the parameters are set right before loading the project.
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2322
<tr><td colspan=2><i>If a project <b>is</b> loaded into the database, you will see:</i>
2423
<tr><td valign=top>Remove from database<td valign=top>The sequences and annotation will be removed, but the files stay on disk.
25-
<tr><td valign=top>Reload project<td valign=top>Executes "Remove project from database" followed by "Load project".
24+
<tr><td valign=top>Reload project<td valign=top>Executes "Remove project from database" followed by "Load project".
2625
<br>If there are
2726
alignment files, you will be asked if you want them removed; if your sequences or grp_prefix (see parameters) have
2827
changed, say 'yes' as the alignment needs to be run again.
29-
<tr><td valign=top>Reload annotation<td valign=top>Removes and then load the annotations.
30-
<br>The "Alignment & Synteny" commands will
31-
recognize that the alignments have already be performed and will only perform the synteny computation. If you
28+
<tr><td valign=top>Reload annotation<td valign=top>Removes and then load the annotations.
29+
<br>The "Alignment & Synteny" commands will
30+
recognize that the alignments have already be performed and will only perform the synteny computation. If you
3231
want the alignments to be re-run, you need to "Clear" each respective cell.
33-
<tr><td valign=top>Parameters<td valign=top>After the project is loaded, you can still change the Summary parameters.
32+
<tr><td valign=top>Parameters<td valign=top>After the project is loaded, you can still change the Summary parameters.
3433
</table>
3534
<p>
3635

3736
</div>
3837

3938
<h2>Available Synteny Section</h2>
4039
<div style="width:500px">
40+
Sequence alignments are performed with
41+
<a href="http://mummer.sourceforge.net/manual">MUMmer3</a>,
42+
but can be changed to use
43+
<a href="https://mummer4.github.io">MUMmer4</a> (see SyMAP
44+
<a href="https://csoderlund.github.io/SyMAP/MUMmer.html">MUMmer</a>).
45+
BLAT is used for FPC alignments (FPC alignments are probably obsolete now).
46+
47+
<p>
4148
This section shows a table with the status of alignments between
4249
the selected projects. (Only projects loaded to the database are shown.)
43-
<p>
4450
Each cell in the table represents a pair of projects (labeled on the
4551
rows and columns) and the cell contains a status code showing
4652
whether or not that pair has been aligned (codes are listed below). Note that the table
4753
actually shows each pair twice, but only the lower cells are activated.
4854
<p>
49-
Clicking on a cell selects that pair of projects (the cell then highlights in yellow).
55+
Clicking on a cell selects that pair of projects (the cell then highlights in yellow).
5056
Alignment and synteny may then be computed or viewed for that particular pair, using
5157
the function buttons (described below). If no cell is selected, you can still
52-
use some of the function buttons, which apply to all the cells.
58+
use some of the function buttons, which apply to all the cells.
5359
</div>
5460

5561
<p>
@@ -77,7 +83,7 @@ <h2>Available Synteny Section</h2>
7783
A
7884
</td>
7985
<td align="left" valign="top" width="550" >
80-
The alignment (MUMmer or BLAT) has been performed but the anchors have not been
86+
The MUMmer alignment (BLAT for FPC-Seq) has been performed but the anchors have not been
8187
loaded and the synteny computation has not been run. This status occurs if
8288
a pair is completed but then annotations are re-loaded for one of the projects,
8389
or if the MUMmer files have been added by the user (see website "System Guide" for details).
@@ -91,7 +97,7 @@ <h2>Available Synteny Section</h2>
9197
<td align="left" valign="top" width="550" >
9298
SyMAP puts an empty file with the name 'all.done' in the /align directory to indicate
9399
all alignments successfully completed. If this file is not present, the alignment
94-
may not have completed. In this case, any alignments will be completed and the
100+
may not have completed. In this case, any alignments will be completed and the
95101
synteny run.
96102
</td>
97103
</tr>
@@ -105,9 +111,9 @@ <h2>Available Synteny Section</h2>
105111
</tr>
106112
</table>
107113
<p>
108-
<b> CPUs:</b> Enter the maximum number of CPUs to use for an alignment. SyMAP will use
114+
<b> CPUs:</b> Enter the maximum number of CPUs to use for an alignment. SyMAP will use
109115
up to that number (but may use fewer, depending on the number of sequences being aligned). Alternatively,
110-
the number of CPUs may be entered as a command line argument (-p N)
116+
the number of CPUs may be entered as a command line argument (-p N)
111117
or entered in the symap.config file; this second option will retain the setting between sessions.
112118
<p><b> Concat:</b>The chromosomes (and/or scaffolds) are concatenated together for one genome
113119
and searched against the chromosomes of the 2nd genome. If this is unchecked, then each chromosome
@@ -128,17 +134,17 @@ <h2>Available Synteny Section</h2>
128134
</tr>
129135
<tr>
130136
<td align="center" valign="top" colspan=2>
131-
<i>Alignment & Synteny</i>
137+
<i>Alignment & Synteny</i>
132138
</td>
133139
</tr>
134140
<tr>
135141
<td align="left" valign="top">
136142
All Pairs
137143
</td>
138144
<td align="left" valign="top" width="550" >
139-
Run (or complete) the synteny computation for all pairs in the Available Syntenies table.
145+
Run (or complete) the synteny computation for all pairs in the Available Syntenies table.
140146
However, this will not run 'self-syntenies'; those need to be done individually by selecting
141-
the pair. Also, a draft sequence can only be aligned to one complete sequence, so those
147+
the pair. Also, a draft sequence can only be aligned to one complete sequence, so those
142148
should also be done individually.
143149
</td>
144150
</tr>
@@ -147,33 +153,33 @@ <h2>Available Synteny Section</h2>
147153
Selected Pair
148154
</td>
149155
<td align="left" valign="top" width="550" >
150-
Run (or complete) the alignment & synteny computation for the selected project pair.
151-
If the pair is already complete, the button label changes to "Re-do", and
156+
Run (or complete) the alignment & synteny computation for the selected project pair.
157+
If the pair is already complete, the button label changes to "Re-do", and
152158
the function is to re-run the synteny computation only. If you wish to re-run
153-
the BLAT or MUMmer alignment also, first use the "Clear Pair" function.
159+
the BLAT or MUMmer alignment also, first use the "Clear Pair" function.
154160
</td>
155161
</tr>
156162
<tr>
157163
<td align="left" valign="top">
158164
Clear Pair
159165
</td>
160166
<td align="left" valign="top" width="550" >
161-
Fully reset the selected pair, removing its synteny results and its MUMmer or BLAT
162-
alignment files.
167+
Fully reset the selected pair, removing its synteny results and its MUMmer or BLAT
168+
alignment files.
163169
</td>
164170
</tr>
165171
<tr>
166172
<td align="left" valign="top">
167173
Parameters
168174
</td>
169175
<td align="left" valign="top" width="550" >
170-
Set alignment & synteny parameters for the selected pair cell (has its own help window).
176+
Set alignment & synteny parameters for the selected pair cell (has its own help window).
171177
</td>
172178
</tr>
173179

174180
<tr>
175181
<td align="center" valign="top" colspan=2>
176-
<i>Display for Selected Pair</i>
182+
<i>Display for Selected Pair</i>
177183
</td>
178184
</tr>
179185
<tr>
@@ -190,15 +196,15 @@ <h2>Available Synteny Section</h2>
190196
</td>
191197
<td align="left" valign="top" width="550" >
192198
A linear display showing synteny blocks of one project aligned
193-
next to the chromosomes of the other.
199+
next to the chromosomes of the other.
194200
</td>
195201
</tr>
196202
<tr>
197203
<td align="left" valign="top">
198204
Circle View
199205
</td>
200206
<td align="left" valign="top" width="550" >
201-
Circular display (Circos-style)
207+
Circular display (Circos-style)
202208
</td>
203209
</tr>
204210
<tr>
@@ -211,7 +217,7 @@ <h2>Available Synteny Section</h2>
211217
</tr>
212218
<tr>
213219
<td align="center" valign="top" colspan=2>
214-
<i>Display for All Projects</i>
220+
<i>Display for All Projects</i>
215221
</td>
216222
</tr>
217223
<tr>
@@ -226,7 +232,7 @@ <h2>Available Synteny Section</h2>
226232
</tr>
227233
<tr>
228234
<td align="center" valign="top" colspan=2>
229-
<i>For Seq-to-Seq Pairs</i>
235+
<i>For Seq-to-Seq Pairs</i>
230236
</td>
231237
</tr>
232238
<tr>
@@ -238,5 +244,9 @@ <h2>Available Synteny Section</h2>
238244
and other valuable synteny-derived information. This does not work for self-synteny or FPC-to-Seq.
239245
</td>
240246
</tr>
247+
</table>
248+
<p>
249+
250+
</div>
241251
</body>
242-
</html>
252+
</html>

‎java/src/html/ProjMgrInstruct.html‎

Lines changed: 7 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -5,13 +5,15 @@
55

66
<h2>SyMAP Project Manager</h2>
77
<p>
8-
Select one or more projects from the list on the left, or
9-
create a new project using the Add Project button at the lower left.
8+
<b>Build</b>: For instructions on building a SyMAP synteny alignment,
9+
click <a href="https://csoderlund.github.io/SyMAP/SystemGuide.html">System Guide</a>
10+
to open the online system manual in a web browser.
1011
<p>
12+
<b>View</b>: Select two or more projects on the left.
1113
For more help, use the Help buttons on each individual window, or
12-
click <a href="http://www.agcol.arizona.edu/software/symap/doc/UserGuide.html">User Guide</a>
14+
click <a href="https://csoderlund.github.io/SyMAP/UserGuide.html">User Guide</a>
1315
to open the online user manual in a web browser.
14-
16+
<p>
1517
</div>
1618
</body>
17-
</html>
19+
</html>

‎java/src/symap/SyMAP.java‎

Lines changed: 10 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -25,16 +25,21 @@
2525
* be properly set along with all of the corresponding .properties files.
2626
*/
2727
public class SyMAP {
28-
public static final String VERSION = "v5.0.8";
29-
public static final String DATE = " (1-June-22)";
28+
public static final String VERSION = "v5.1.0";
29+
public static final String DATE = " (12-June-22)";
3030
public static final int DBVER = 2;
3131
public static final String DBVERSTR = "db" + DBVER;
3232

33-
// CAS500 change v4.2 to doc
34-
public static final String BASE_HELP_URL = "http://www.agcol.arizona.edu/software/symap/doc/";
33+
// CAS500 change v4.2 to doc; CAS510 change base to github; put #links here
34+
public static final String BASE_HELP_URL_prev51 = "http://www.agcol.arizona.edu/software/symap/doc/";
35+
public static final String BASE_HELP_URL = "https://csoderlund.github.io/SyMAP/"; // CAS510
3536
public static final String USER_GUIDE_URL = BASE_HELP_URL + "UserGuide.html";
37+
public static final String circle = "#circle";
38+
public static final String dotplot = "#dotplot_display";
39+
public static final String align2d = "#alignment_display_2d";
40+
public static final String align3d = "#alignment_display_3d";
3641
public static final String TROUBLE_GUIDE_URL = BASE_HELP_URL + "TroubleShoot.html";
37-
42+
3843
public static final int MAX_PROJECTS = 100; // for parsing applet params
3944

4045
private static final int REQUIRED_JAVA_MAJOR_VERSION = 1;

‎java/src/symap/frame/ControlPanel.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -88,7 +88,7 @@ public ControlPanel(DrawingPanel dp, HistoryControl hc, ImageViewer iv,
8888
bar,null,false);
8989
helpButton.addActionListener(new ActionListener() {
9090
public void actionPerformed(ActionEvent e) {
91-
String url = SyMAP.USER_GUIDE_URL + "#alignment_display_2d";
91+
String url = SyMAP.USER_GUIDE_URL + SyMAP.align2d; // CAS510
9292
if ( !Utilities.tryOpenURL(url) )
9393
System.err.println("Error opening URL: " + url);
9494
}

‎java/src/symap/projectmanager/common/ProjectManagerFrameCommon.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -62,7 +62,7 @@ public class ProjectManagerFrameCommon extends JFrame implements ComponentListen
6262
/************************************************/
6363
private static final String HTML = "/html/ProjMgrInstruct.html";
6464
private static final String WINDOW_TITLE = "SyMAP " + SyMAP.VERSION + " Project Manager";
65-
private final String DB_ERROR_MSG = "A database error occurred, please see the Troubleshooting Guide at:\n" + SyMAP.TROUBLE_GUIDE_URL + "#database_error";
65+
private final String DB_ERROR_MSG = "A database error occurred, please see the Troubleshooting Guide at:\n" + SyMAP.TROUBLE_GUIDE_URL;
6666
private final String DATA_PATH = Constants.dataDir;
6767

6868
private final int MIN_WIDTH = 900;

‎java/src/symap3D/SyMAPFrame3D.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -251,7 +251,7 @@ public String getHelpText(MouseEvent e) {
251251
helpButton.setMargin(new Insets(4, 3, 4, 3));
252252
helpButton.addActionListener(new ActionListener() {
253253
public void actionPerformed(ActionEvent e) {
254-
String url = SyMAP.USER_GUIDE_URL + "#alignment_display_3d";
254+
String url = SyMAP.USER_GUIDE_URL + SyMAP.align3d; // CAS510
255255
if ( !Utilities.tryOpenURL(url) )
256256
System.err.println("Error opening URL: " + url);
257257
}

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