Minor updates to design docs - DOC

613d48a2 · Gemma Guest · d018cfdc · 613d48a2 · 613d48a2 · d018cfdc
Commit 613d48a2 authored 8 years ago by Gemma Guest
--- a/src/doc/Design_notes/architecture.html
+++ b/src/doc/Design_notes/architecture.html
@@ -14,7 +14,6 @@
        <a href="modules/dotterApp.html">dotterApp</a>: dotter application code<br />
        <a href="modules/belvuApp.html">belvuApp</a>: belvu application code<br />
        <a href="modules/seqtoolsUtils.html">seqtoolsUtils</a>: generic utilities<br />
-        <a href="modules/libpfetch.html">libpfetch</a>: utilities for fetching over http (only required for blixemh: requires libcurl)<br />
      </p>
    </div>
  </p>

--- a/src/doc/Design_notes/build.html
+++ b/src/doc/Design_notes/build.html
@@ -6,7 +6,7 @@
 <body>
 <div class="outer">
  <h1>Build System</h1>
-  This page describes how to compile the SeqTools package using the Autotools scripts included with the source code.
+  This page describes how to compile the SeqTools package from the development repository (as opposed to the dist file) using the Autotools scripts included with the source code.

  <h2>Autotools</h2>
  <p>
@@ -16,15 +16,15 @@
      <li>src/configure.ac: This file is processed by autoconf to produce the configure file.
      <li>src/Makefile.am: This file is processed by automake to produce the Makefile.in file.
      <li>src/AUTHORS, src/COPYING, src/README, src/NEWS, src/ChangeLog: These files are for information.
-      <li>subdirectory Makefile.am files: The subdirectories blixemApp, dotterApp, seqtoolsUtils and libpfetch all contain a Makefile.am file, which is processed by automake to create a Makefile.in file in that directory.
+      <li>subdirectory Makefile.am files: The subdirectories blixemApp, dotterApp and seqtoolsUtils all contain a Makefile.am file, which is processed by automake to create a Makefile.in file in that directory.
    </ul>
  </p>

  <p>
    The build process is as follows:
    <ul>
-      <li>Run '<code>autoreconf -i</code>' in the <code>src</code> directory. This runs autoheader, aclocal, autoconf and automake and creates the configure script (and some other required files) in the src directory.
-      <li><code>cd</code> to the directory where the code is to be built (this can be src or any other directory, e.g. src/build) and run the configure script from there. This will create a makefile in the build directory (and subdirectories for blixemApp, dotterApp, seqtoolsUtils and libpfetch, which all contain a makefile for building that module). It will also create the config.h file that will be included by the code, and a few other required files.
+      <li>Run '<code>./autogen.sh</code>' in the <code>src</code> directory. This runs autoheader, aclocal, autoconf and automake and creates the configure script (and some other required files) in the src directory. It also clones the gbtools library and configures that.
+      <li><code>cd</code> to the directory where the code is to be built (this can be src or any other directory, e.g. src/build) and run the <code>runconfig.sh</code> script from there. This will create a makefile in the build directory (and subdirectories for blixemApp, dotterApp and seqtoolsUtils, which all contain a makefile for building that module). It will also create the config.h file that will be included by the code, and a few other required files.
      <li>Run <code>make</code> in the build directory to build everything (or in a subdirectory to build just that module).
    </ul>
  </p>
@@ -37,8 +37,7 @@
      <li>dotterApp: Dotter application code.
      <li>seqtoolsUtils: Generic utility functions. Required by dotter, blixem and blixemh.
      <li>seqtoolsUtils: Generic seqtools utility functions. Required by dotter, blixem and blixemh.
-      <li>libpfetch: Utilities for fetching sequences over http. Required by blixemh.
-      <li>gbtools: Generic utility functions from an external repository of shared code. This code is included in the distribution so that it is automatically compiled as part of the seqtools package.
+      <li>gbtools: Generic utility functions from an external repository of shared code. This code is included in the distribution so that it is automatically compiled as part of the seqtools package. See the <code>src/INSTALL.DEVELOPER</code> file for more information about including gbtools.
    </ul>
  </p>

@@ -48,6 +47,7 @@
      <li>All of the executables in the SeqTools package require the GLib and GTK+ libraries. These are built using pkg-config. configure.ac specifies which version of the libraries are required.
      <li>blixemh uses the libpfetch library, which requires the libcurl library.
      <li>blixem and blixemh compile in the sqlite3 library if it is availble. If it is not available, the sqlite functionality is disabled.
+      <li>See the INSTALL.XXX files for more information about dependencies.
    </ul>
  </p>
 </div>

--- a/src/doc/Design_notes/modules/libpfetch.html
+++ b/src/doc/Design_notes/modules/libpfetch.html
-<head>
-  <title>SeqTools - libpfetch</title>
-</head>
-
-
-<body>
-<div class="outer">
-  <h1>libpfetch</h1>
-  <p>This module provides utilities for fetching sequences over http.  This functionality is only required by blixemh - the libpfetch code is conditionally compiled into blixemh using the PFETCH_HTML flag.  Note that use of libpfetch introduces a dependency on libcurl - the development version of libcurl must be installed in order to compile blixemh.</p>
-
-</div>
-</body>
--- a/src/doc/User_doc/todo.html
+++ b/src/doc/User_doc/todo.html
@@ -10,21 +10,16 @@
  <ul>
    <li>Issues
    <ul>
-      <li>Variations: the variations track is experimental code and will need to be improved, in particular in its handling of overlapping features.
-      <li>Feature-series: this functionality was disabled when Blixem and Dotter were re-written at version 4. We should consider whether this is still a useful feature and, if so, whether to use the original SFS file format or to switch to GFF.  The SFS file format is documented <a href="http://sfixem.sbc.su.se/SFS_desc.html">here</a>.
      <li>Multiple row selections: using the up/down arrow keys to move the row selection doesn't always work if there are adjacent rows from the same match sequence.
-      <li>DNA search: this currently just jumps to the start of the DNA section that was found; we should also highlight the found DNA in the reference sequence.
      <li>Printing: the pfetch window should have a print option.
    </ul>
    <br/>
    <li>Enhancements
    <ul>
-      <li>It would be nice to be able to view the sequence data for an insertion (a vertical yellow line in a match sequence) in Blixem, e.g. by hovering over it with the mouse.
-      <li>When you hover over an exon in the exon view in Blixem (when bumped), it would be nice if info about the exon were shown in the toolbar feedback area.
+      <li>It would be nice to be able to view the sequence data for an insertion (a vertical purple line in a match sequence) in Blixem, e.g. by hovering over it with the mouse.
+      <li>Bumping the gene model section should be improved so that different featuresets can be bumped separately. It would also be good to show information about the features in this section in the feedback area when you mouse-over them.
      <li>When running Dotter on a large range it takes a long time to start up and there is no indication that anything is happening; it would be good to have a status bar of some description, and a cancel button. When running from Blixem, we should report if Dotter fails to start.
-      <li>When calling Dotter from Blixem, start Dotter with the crosshair placed at the currently-selected coords in Blixem (if applicable).
-      <li>Cosmetic: the %ID labels on the big picture grid should be right-aligned.
-      <li>Button tooltips: the zoom buttons in the big-picture should have tooltips.
+      <li>Better Blixem<->Dotter interactions, ideally full two-way communications, or at least when calling Dotter from Blixem it would be good to start Dotter with the crosshair placed at the currently-selected coords in Blixem (if applicable).
    </ul>
  </ul>

@@ -32,7 +27,7 @@
  <ul>
    <li>Issues
    <ul>
-      <li>There is a bug where the dot-plot can appear blacked-out if the plot is very wide and you zoom in (say to about half of the default compression factor).
+      <li>There is an intermittent bug where the dot-plot can appear blacked-out if the plot is very wide and you zoom in (say to about half of the default compression factor).
    </ul>
    <br/>
    <li>Enhancements
@@ -49,6 +44,7 @@
      <li>In the colour-by-conservation colour schemes, the foreground colour is tied to the background colour.  This means that if the same background colour is specified more than once, the foreground colours are ambiguous.
      <li>Colours dialog: the dialog for editing the residue colours used to have a section at the bottom showing residues grouped by colour. This has not been implemented in the new Belvu yet.
      <li>For short alignments, the initial window size is too large.
+      <li>There is a bug with changing the font size on Mac OS X, where the highlighting does not line up correctly with the text if the font size is not a multiple of 4.
    </ul>
    <br/>
    <li>Enhancements